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authorbicatali <bicatali@32389bae-6d03-0410-99cf-db05cde120eb>2008-03-17 16:21:32 +0000
committerbicatali <bicatali@32389bae-6d03-0410-99cf-db05cde120eb>2008-03-17 16:21:32 +0000
commit76ffb781ed7a917f23b67454e9f950e5e3b83527 (patch)
tree94fa8e1ddc7cb9ef80b78ea7896a5845f074f95b
parentmove stuff to root (diff)
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-rw-r--r--sys-cluster/empi/files/README.txt75
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-rw-r--r--sys-cluster/lam-mpi/ChangeLog302
-rw-r--r--sys-cluster/lam-mpi/Manifest8
-rw-r--r--sys-cluster/lam-mpi/files/7.1.2-lam_prog_f77.m4.patch11
-rw-r--r--sys-cluster/lam-mpi/files/7.1.2-liblam-use-extra-libs.patch10
-rw-r--r--sys-cluster/lam-mpi/files/7.1.4-as-needed.patch100
-rw-r--r--sys-cluster/lam-mpi/files/eselect.mpi.lam-mpi7
-rw-r--r--sys-cluster/lam-mpi/lam-mpi-7.1.4-r1.ebuild117
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-rw-r--r--sys-cluster/libibcommon/ChangeLog16
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-rw-r--r--sys-cluster/libibmad/ChangeLog16
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-rw-r--r--sys-cluster/libibmad/libibmad-1.1.2.ebuild29
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-rw-r--r--sys-cluster/libibumad/ChangeLog16
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734 files changed, 22573 insertions, 0 deletions
diff --git a/app-admin/eselect-mpi/ChangeLog b/app-admin/eselect-mpi/ChangeLog
new file mode 100644
index 000000000..fadac87aa
--- /dev/null
+++ b/app-admin/eselect-mpi/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for app-admin/eselect-mpi
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 29 Feb 2008; Justin Bronder <jsbronder@gentoo.org> ChangeLog:
+ Initial import
+
diff --git a/app-admin/eselect-mpi/Manifest b/app-admin/eselect-mpi/Manifest
new file mode 100644
index 000000000..22a86472e
--- /dev/null
+++ b/app-admin/eselect-mpi/Manifest
@@ -0,0 +1,5 @@
+AUX mpi.eselect-0.0.1 5906 RMD160 50fe1e3bbd33b53ff1e991559833fdc1d3a29786 SHA1 d50f55983ae7b04ac307ee8d0f76f11796116dcb SHA256 75371c29d48487f8271cc7cd52ee433f01ba902e1977cad34cb0816164e52835
+AUX mpi.eselect-0.0.2 6241 RMD160 8d156a0c6f4a0726b58f23f7e61ea0ae443529ad SHA1 a8da7af051d30fe039d850fab306bcf12bb133b7 SHA256 a5c98c1af12145b489f9c7ef5bb7c822e835496d9024b2e6a00246cc4382f92b
+EBUILD eselect-mpi-0.0.1.ebuild 471 RMD160 a0ebe2dd4b15145b4b59ba3315e024bc40d5c666 SHA1 3ea3e291035938ea60cd6317d567dd4a6bbe8bcf SHA256 2b8e45415133a5c7af1c83b088e68a01e7a7671e0e1ad300fd73f5a567ed797f
+EBUILD eselect-mpi-0.0.2.ebuild 471 RMD160 a0ebe2dd4b15145b4b59ba3315e024bc40d5c666 SHA1 3ea3e291035938ea60cd6317d567dd4a6bbe8bcf SHA256 2b8e45415133a5c7af1c83b088e68a01e7a7671e0e1ad300fd73f5a567ed797f
+MISC ChangeLog 204 RMD160 2942e0f3e4c22cc4de7fbd3cac7c4782a9a1277b SHA1 6f370d97e1ba7f201511f9076be8792b2f4a7681 SHA256 61111109097ea69c5124a0297fe5776115fae9e60e3097eaa9e966a1e3586f30
diff --git a/app-admin/eselect-mpi/eselect-mpi-0.0.1.ebuild b/app-admin/eselect-mpi/eselect-mpi-0.0.1.ebuild
new file mode 100644
index 000000000..7a6d8f600
--- /dev/null
+++ b/app-admin/eselect-mpi/eselect-mpi-0.0.1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="eselect-mpi"
+HOMEPAGE="localhost"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64"
+IUSE=""
+
+DEPEND="app-admin/eselect"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ local MODULEDIR="/usr/share/eselect/modules"
+ local MODULE="mpi"
+ dodir ${MODULEDIR}
+ insinto ${MODULEDIR}
+ newins "${FILESDIR}"/${MODULE}.eselect-${PVR} ${MODULE}.eselect
+}
+
diff --git a/app-admin/eselect-mpi/eselect-mpi-0.0.2.ebuild b/app-admin/eselect-mpi/eselect-mpi-0.0.2.ebuild
new file mode 100644
index 000000000..7a6d8f600
--- /dev/null
+++ b/app-admin/eselect-mpi/eselect-mpi-0.0.2.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="eselect-mpi"
+HOMEPAGE="localhost"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64"
+IUSE=""
+
+DEPEND="app-admin/eselect"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ local MODULEDIR="/usr/share/eselect/modules"
+ local MODULE="mpi"
+ dodir ${MODULEDIR}
+ insinto ${MODULEDIR}
+ newins "${FILESDIR}"/${MODULE}.eselect-${PVR} ${MODULE}.eselect
+}
+
diff --git a/app-admin/eselect-mpi/files/mpi.eselect-0.0.1 b/app-admin/eselect-mpi/files/mpi.eselect-0.0.1
new file mode 100644
index 000000000..098110358
--- /dev/null
+++ b/app-admin/eselect-mpi/files/mpi.eselect-0.0.1
@@ -0,0 +1,235 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id: $
+
+DESCRIPTION="Manage MPI implementations"
+MAINTAINER="jsbronder@gentoo.org"
+SVN_DATE='$Date: $'
+VERSION="0.0.1"
+
+inherit path-manipulation config
+
+# The basic idea is we want to allow every use to select their own mpi
+# implementation they want, and a ${HOME}/.env.d/mpi file is created for them.
+# A user then is -required- to source the env file. This sets PATH, MANPATH,
+# and LD_LIBRARY_PATH. I'm sure I'm forgetting something here.
+# Calling unset only wipes out the env file, replacing it with what we
+# previously added stripped out.
+
+# If you can think of a better way to do this, while still allowing user's
+# freedom, please let me know.
+
+# List the valid mpi implementations currently installed.
+find_implementations() {
+ local imps
+ for f in ${ROOT}/etc/env.d/mpi/*; do
+ [[ -f ${f} ]] || continue
+ f=$(basename ${f})
+ [[ "${f#mpi-}" == "${f}" ]] && continue
+ imps=(${imps[@]} ${f})
+ done
+ echo ${imps[@]}
+}
+
+# User's current environment has the implementation configured in it.
+is_in_use() { [ "${ESELECT_MPI_IMP}" == "${1}" ]; }
+
+# User's env file is ready for sourcing for this implementation.
+is_enabled() {
+ [ "$(var_from_user_envd ESELECT_MPI_IMP)" == "${1}" ]
+}
+
+var_from_user_envd(){
+ [ ! -f ${user_ev} ] && return 0
+ echo "$(source ${user_ev}; echo ${!1})"
+}
+
+# Is this a valid implementation?
+is_implementation() {
+ local imps=$(find_implementations)
+ for i in ${imps[@]}; do
+ [[ "${i}" == "${1}" ]] && return 0
+ done
+ return 1
+}
+
+init() {
+ local d
+ [[ ${UID} -eq 0 ]] && HOME="${ROOT}/root"
+ d="$(canonicalise "${ROOT}/${HOME}")"
+ user_ev="${d}/.env.d/mpi";
+
+ if [[ ! -d "${d}" ]]; then
+ mkdir "${d}" || die -q "Failed to create ${d}."
+ elif [[ ! -w "${d}" ]]; then
+ die -q "You do not have permission to mkdir ${d}."
+ fi
+ [[ -f "${f}" && ! -w "${f}" ]] && die -q "You do not have permission to write to ${f}."
+}
+
+global_env() {
+ local d=$(canonicalise "${ROOT}/etc/env.d/mpi/${1}")
+ [ -z "${d}" ] && die "Cannot find global env file for ${1}"
+ ev=${d}
+}
+
+clean_var() {
+ local imp v
+ local value="${!1}"
+ local d="$(canonicalise "${ROOT}/etc/env.d/mpi/${imp}")"
+ [ -z "${value}" ] && return 0
+ [ -z "${d}" ] && continue
+
+ for imp in $(find_implementations); do
+ v=$(load_config ${d}/${imp} ${1})
+ [ -z "${v}" ] && continue
+ value="$(echo ${value} | sed -e "s|${v}:||g")"
+ done
+ echo ${value}
+}
+
+
+### list action ###
+
+describe_list() { echo "List available implementations"; }
+describe_list_parameters() { echo "[-p]"; }
+
+do_list() {
+ imps=( $(find_implementations) )
+ init
+ if [[ ${@} == *-p* ]]; then
+ echo "${imps[@]}"
+ else
+ write_list_start "Available MPI implementations:"
+ if [[ -n "${imps[@]}" ]]; then
+ for (( i=0; i<${#imps[@]}; i++ )); do
+ if is_in_use ${imps[$i]} && is_enabled ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "Enabled, In Use"
+ elif is_in_use ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "In Use"
+ elif is_enabled ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "Enabled"
+ else
+ write_kv_list_entry "${imps[$i]}" "--"
+ fi
+ done
+ else
+ write_kv_list_entry "(none found)" ""
+ fi
+ fi
+ return 0
+}
+
+
+### set action ###
+
+describe_set() {
+ echo "Select a MPI implementation."
+}
+
+describe_set_parameters() {
+ echo "<target>"
+}
+
+do_set() {
+ local binpath lld manpath
+
+ init
+ global_env ${1}
+
+ [[ -z ${1} ]] && die -q "You didnt specifiy any implementation for use."
+ [[ ${#@} -ne 1 ]] && die -q "You may only select exactly one implementation."
+ ! is_implementation ${1} && die -q "${1} is not an implementation."
+ is_enabled ${1} && return 0
+
+ binpath="$(load_config ${ev} PATH):$(clean_var PATH)"
+ lld="$(load_config ${ev} LD_LIBRARY_PATH):$(clean_var LD_LIBRARY_PATH)"
+ manpath="$(load_config ${ev} MANPATH):$(clean_var MANPATH)"
+
+cat <<-EOF >${user_ev}
+PATH="${binpath}"
+MANPATH="${manpath}"
+LD_LIBRARY_PATH="${lld}"
+ESELECT_MPI_IMP="${1}"
+export LD_LIBRARY_PATH
+export PATH
+export MANPATH
+export ESELECT_MPI_IMP
+EOF
+ echo "Remember to source ${user_ev}"
+}
+
+
+### unset action ###
+describe_unset() {
+ echo "Restore MPI-less environment."
+}
+
+do_unset() {
+ local binpath lld manpath
+
+ init
+
+ binpath="$(clean_var PATH)"
+ lld="$(clean_var LD_LIBRARY_PATH)"
+ manpath="$(clean_var MANPATH)"
+cat <<-EOF >${user_ev}
+PATH="${binpath}"
+MANPATH="${manpath}"
+LD_LIBRARY_PATH="${lld}"
+export LD_LIBRARY_PATH
+export PATH
+export MANPATH
+unset ESELECT_MPI_IMP
+EOF
+ echo "Remember to source ${user_ev}"
+}
+
+### add action (from skel pretty much)
+describe_add() {
+ echo "Add a new mpi implementation"
+}
+
+describe_add_parameters() {
+ echo "<file>"
+}
+
+do_add() {
+ local imp
+ [[ ${#@} -ne 1 ]] \
+ && die -q "Bad arguments, use: mpi add /some/full/path/<implementation>.eselect"
+
+ # If $D is set, we're adding from portage so we want to respect sandbox.
+ # Otherwise, respect the ROOT variable.
+ local PREFIX=${D:-${ROOT}/}
+
+ # Create directory if necessary
+ if [[ ! -e ${PREFIX}/etc/env.d/mpi/ ]]; then
+ mkdir -p ${PREFIX}/etc/env.d/mpi/
+ else
+ if [[ ! -d ${PREFIX}/etc/env.d/mpi/ ]]; then
+ die -q "${PREFIX}/etc/env.d/mpi/ exists but isn't a directory!"
+ fi
+ fi
+
+ imp=$(basename ${1}); imp=${imp%.eselect}
+ if ! cp ${1} ${PREFIX}/etc/env.d/mpi/${imp}; then
+ die -q "Installing ${1} as ${PREFIX}/etc/env.d/mpi/${imp} failed!"
+ fi
+}
+
+
+### printvar action ###
+describe_printvar() { echo "Print variables stored in global env.d file."; }
+describe_printvar_parameters() { echo "<implementation> <variable>"; }
+
+do_printvar() {
+ if [[ ${#@} -ne 2 ]] \
+ || ! is_implementation ${1}; then
+ die -q "Specify exactly 1 implementation and 1 variable."
+ fi
+ global_env ${1}
+ echo "$(load_config ${ev} ${2})"
+}
+
+# vim: set ft=eselect :
diff --git a/app-admin/eselect-mpi/files/mpi.eselect-0.0.2 b/app-admin/eselect-mpi/files/mpi.eselect-0.0.2
new file mode 100644
index 000000000..4f000c9df
--- /dev/null
+++ b/app-admin/eselect-mpi/files/mpi.eselect-0.0.2
@@ -0,0 +1,237 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id: $
+
+DESCRIPTION="Manage MPI implementations"
+MAINTAINER="jsbronder@gentoo.org"
+SVN_DATE='$Date: $'
+VERSION="0.0.2"
+
+inherit path-manipulation config
+
+# The basic idea is we want to allow every use to select their own mpi
+# implementation they want, and a ${HOME}/.env.d/mpi file is created for them.
+# A user then is -required- to source the env file. This sets PATH, MANPATH,
+# and LD_LIBRARY_PATH. I'm sure I'm forgetting something here.
+# Calling unset only wipes out the env file, replacing it with what we
+# previously added stripped out.
+
+# If you can think of a better way to do this, while still allowing user's
+# freedom, please let me know.
+
+# List the valid mpi implementations currently installed.
+find_implementations() {
+ local imps
+ for f in ${ROOT}/etc/env.d/mpi/*; do
+ [[ -f ${f} ]] || continue
+ f=$(basename ${f})
+ [[ "${f#mpi-}" == "${f}" ]] && continue
+ imps=(${imps[@]} ${f})
+ done
+ echo ${imps[@]}
+}
+
+# User's current environment has the implementation configured in it.
+is_in_use() { [ "${ESELECT_MPI_IMP}" == "${1}" ]; }
+
+# User's env file is ready for sourcing for this implementation.
+is_enabled() {
+ [ "$(var_from_user_envd ESELECT_MPI_IMP)" == "${1}" ]
+}
+
+var_from_user_envd(){
+ [ ! -f ${user_ev} ] && return 0
+ echo "$(source ${user_ev}; echo ${!1})"
+}
+
+# Is this a valid implementation?
+is_implementation() {
+ local imps=$(find_implementations)
+ for i in ${imps[@]}; do
+ [[ "${i}" == "${1}" ]] && return 0
+ done
+ return 1
+}
+
+init() {
+ local d
+ [[ ${UID} -eq 0 ]] && HOME="${ROOT}/root"
+ d="$(canonicalise "${ROOT}/${HOME}")"
+ d="${d}/.env.d/"
+ user_ev="${d}mpi";
+
+ if [[ ! -d "${d}" ]]; then
+ mkdir "${d}" || die -q "Failed to create ${d}."
+ elif [[ ! -w "${d}" ]]; then
+ die -q "You do not have permission to mkdir ${d}."
+ fi
+ [[ -f "${user_ev}" && ! -w "${user_ev}" ]] \
+ && die -q "You do not have permission to write to ${user_ev}."
+}
+
+global_env() {
+ local d=$(canonicalise "${ROOT}/etc/env.d/mpi/${1}")
+ [ -z "${d}" ] && die "Cannot find global env file for ${1}"
+ ev=${d}
+}
+
+clean_var() {
+ local imp v
+ local value="${!1}"
+ local d="$(canonicalise "${ROOT}/etc/env.d/mpi/${imp}")"
+ [ -z "${value}" ] && return 0
+ [ -z "${d}" ] && continue
+
+ for imp in $(find_implementations); do
+ v=$(load_config ${d}/${imp} ${1})
+ [ -z "${v}" ] && continue
+ value="$(echo ${value} | sed -e "s|${v}:||g")"
+ done
+ echo ${value}
+}
+
+
+### list action ###
+
+describe_list() { echo "List available implementations"; }
+describe_list_parameters() { echo "[-p]"; }
+
+do_list() {
+ imps=( $(find_implementations) )
+ init
+ if [[ ${@} == *-p* ]]; then
+ echo "${imps[@]}"
+ else
+ write_list_start "Available MPI implementations:"
+ if [[ -n "${imps[@]}" ]]; then
+ for (( i=0; i<${#imps[@]}; i++ )); do
+ if is_in_use ${imps[$i]} && is_enabled ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "Enabled, In Use"
+ elif is_in_use ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "In Use"
+ elif is_enabled ${imps[$i]}; then
+ write_kv_list_entry "${imps[$i]}" "Enabled"
+ else
+ write_kv_list_entry "${imps[$i]}" "--"
+ fi
+ done
+ else
+ write_kv_list_entry "(none found)" ""
+ fi
+ fi
+ return 0
+}
+
+
+### set action ###
+
+describe_set() {
+ echo "Select a MPI implementation."
+}
+
+describe_set_parameters() {
+ echo "<target>"
+}
+
+do_set() {
+ local binpath lld manpath
+
+ init
+ global_env ${1}
+
+ [[ -z ${1} ]] && die -q "You didnt specifiy any implementation for use."
+ [[ ${#@} -ne 1 ]] && die -q "You may only select exactly one implementation."
+ ! is_implementation ${1} && die -q "${1} is not an implementation."
+ is_enabled ${1} && return 0
+
+ binpath="$(load_config ${ev} PATH):$(clean_var PATH)"
+ lld="$(load_config ${ev} LD_LIBRARY_PATH):$(clean_var LD_LIBRARY_PATH)"
+ manpath="$(load_config ${ev} MANPATH):$(clean_var MANPATH)"
+
+cat <<-EOF >${user_ev}
+PATH="${binpath}"
+MANPATH="${manpath}"
+LD_LIBRARY_PATH="${lld}"
+ESELECT_MPI_IMP="${1}"
+export LD_LIBRARY_PATH
+export PATH
+export MANPATH
+export ESELECT_MPI_IMP
+EOF
+ echo "Remember to source ${user_ev}"
+}
+
+
+### unset action ###
+describe_unset() {
+ echo "Restore MPI-less environment."
+}
+
+do_unset() {
+ local binpath lld manpath
+
+ init
+
+ binpath="$(clean_var PATH)"
+ lld="$(clean_var LD_LIBRARY_PATH)"
+ manpath="$(clean_var MANPATH)"
+cat <<-EOF >${user_ev}
+PATH="${binpath}"
+MANPATH="${manpath}"
+LD_LIBRARY_PATH="${lld}"
+export LD_LIBRARY_PATH
+export PATH
+export MANPATH
+unset ESELECT_MPI_IMP
+EOF
+ echo "Remember to source ${user_ev}"
+}
+
+### add action (from skel pretty much)
+describe_add() {
+ echo "Add a new mpi implementation"
+}
+
+describe_add_parameters() {
+ echo "<file>"
+}
+
+do_add() {
+ local imp
+ [[ ${#@} -ne 1 ]] \
+ && die -q "Bad arguments, use: mpi add /some/full/path/<implementation>.eselect"
+
+ # If $D is set, we're adding from portage so we want to respect sandbox.
+ # Otherwise, respect the ROOT variable.
+ local PREFIX=${D:-${ROOT}/}
+
+ # Create directory if necessary
+ if [[ ! -e ${PREFIX}/etc/env.d/mpi/ ]]; then
+ mkdir -p ${PREFIX}/etc/env.d/mpi/
+ else
+ if [[ ! -d ${PREFIX}/etc/env.d/mpi/ ]]; then
+ die -q "${PREFIX}/etc/env.d/mpi/ exists but isn't a directory!"
+ fi
+ fi
+
+ imp=$(basename ${1}); imp=${imp%.eselect}
+ if ! cp ${1} ${PREFIX}/etc/env.d/mpi/${imp}; then
+ die -q "Installing ${1} as ${PREFIX}/etc/env.d/mpi/${imp} failed!"
+ fi
+}
+
+
+### printvar action ###
+describe_printvar() { echo "Print variables stored in global env.d file."; }
+describe_printvar_parameters() { echo "<implementation> <variable>"; }
+
+do_printvar() {
+ if [[ ${#@} -ne 2 ]] \
+ || ! is_implementation ${1}; then
+ die -q "Specify exactly 1 implementation and 1 variable."
+ fi
+ global_env ${1}
+ echo "$(load_config ${ev} ${2})"
+}
+
+# vim: set ft=eselect :
diff --git a/app-office/texmacs/ChangeLog b/app-office/texmacs/ChangeLog
new file mode 100644
index 000000000..796ad98be
--- /dev/null
+++ b/app-office/texmacs/ChangeLog
@@ -0,0 +1,293 @@
+# ChangeLog for app-office/texmacs
+# Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*texmacs-1.0.6.12-r1 (09 Jan 2008)
+09 Jan 2008; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.12-r1.ebuild, +files/texmacs-maxima-5.14.0.patch:
+ support for maxima-5.14.0
+
+*texmacs-1.0.6.12 (06 Oct 2007)
+06 Oct 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.12.ebuild -texmacs-1.0.6.11.ebuild
+ -files/texmacs-1.0.6.11-maxima-5.13.0.patch:
+ version bump, cleaning
+
+*texmacs-1.0.6.11 (04 Sep 2007)
+04 Sep 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.11.ebuild:
+ version bump
+
+*texmacs-1.0.6.10-r1 (28 Aug 2007)
+28 Aug 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.10-r1.ebuild, +files/texmacs-maxima-5.13.0.patch,
+ -texmacs-1.0.6.9-r1.ebuild, -files/texmacs-maxima-5.12.0.patch:
+ patch to run maxima-5.13.0 included
+
+*texmacs-1.0.6.10 (15 May 2007)
+ 15 May 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.10.ebuild +files/texmacs-1.0.6.10.patch -texmacs-1.0.6.9.ebuild:
+ Version bump
+
+6 May 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ Added a check that, if guile is 1.8, it is emerged with +deprecated
+
+*texmacs-1.0.6.9-r1 (3 May 2007)
+ 3 May 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ -texmacs-1.0.6.6.ebuild -texmacs-1.0.6.7.ebuild -texmacs-1.0.6.8.ebuild
+ +texmacs-1.0.6.9-r1.ebuild +files/texmacs-maxima-5.12.0.patch:
+ patch to run maxima-5.12.0 included
+
+*texmacs-1.0.6.8 (21 Jan 2007)
+
+ 21 Jan 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.8.ebuild:
+ Version bump
+
+*texmacs-1.0.6.7 (26 Dec 2006)
+
+ 26 Dec 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.7.ebuild -texmacs-1.0.6.2.ebuild -texmacs-1.0.6.3.ebuild
+ -texmacs-1.0.6.4.ebuild -texmacs-1.0.6.5.ebuild:
+ Version bump; USE flag aspell removed (now TeXmacs uses
+ either ispell or aspell automatically); cleaning up old versions
+
+*texmacs-1.0.6.6 (22 August 2006)
+
+ 22 August 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.6.ebuild:
+ Version bump
+
+*texmacs-1.0.6.5 (8 August 2006)
+
+ 8 August 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.5.ebuild:
+ Version bump
+
+*texmacs-1.0.6.4 (27 June 2006)
+
+ 27 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.4.ebuild:
+ Version bump
+
+*texmacs-1.0.6.3 (20 June 2006)
+
+ 20 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.3.ebuild:
+ Version bump
+
+*texmacs-1.0.6.2 (1 June 2006)
+
+ 1 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +texmacs-1.0.6.2.ebuild:
+ Version bump, USE flag to use aspell instead of ispell
+
+ 29 May 2006; Martin Ehmsen <ehmsen@gentoo.org>
+ +files/texmacs-1.0.6-gcc-4.1.patch, texmacs-1.0.6-r1.ebuild:
+ Fixed gcc-4.1 compilation failure, bug #130708.
+
+ 01 May 2006; Martin Ehmsen <ehmsen@gentoo.org> texmacs-1.0.4-r1.ebuild,
+ texmacs-1.0.5.6.ebuild, texmacs-1.0.6-r1.ebuild:
+ Removed libtool from RDEPEND, found by QA script.
+
+*texmacs-1.0.6-r1 (20 Apr 2006)
+
+ 20 Apr 2006; Martin Ehmsen <ehmsen@gentoo.org>
+ +files/texmacs-1.0.6-maxima-5.9.3.patch, -texmacs-1.0.6.ebuild,
+ +texmacs-1.0.6-r1.ebuild:
+ Added patch to make texmacs work with the latest sci-mathematics/maxima
+ (5.9.3), bug #130099.
+
+ 29 Jan 2006; Martin Ehmsen <ehmsen@gentoo.org> files/TeXmacs.desktop,
+ -texmacs-1.0.5.2.ebuild, +texmacs-1.0.6.ebuild:
+ Version bump, bug #112104.
+ Changed the path to the TeXmacs icon in the desktop file.
+ Removed old version that was not ported to modular X.
+
+*texmacs-1.0.6 (29 Jan 2006)
+
+ 25 Jan 2006; Alexandre Buisse <nattfodd@gentoo.org>
+ texmacs-1.0.4-r1.ebuild, texmacs-1.0.5.6.ebuild:
+ Modular X porting.
+
+ 02 Jan 2006; Alexandre Buisse <nattfodd@gentoo.org>
+ texmacs-1.0.4-r1.ebuild, texmacs-1.0.5.2.ebuild, texmacs-1.0.5.6.ebuild:
+ Don't install COPYING and LICENSE files (but COMPILE stays because it has
+ some runtime common bugs explained). Thanks to Markus Ullman in bug #117474.
+
+*texmacs-1.0.5.6 (08 Aug 2005)
+
+ 08 Aug 2005; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.4.7.ebuild,
+ -texmacs-1.0.5.ebuild, +texmacs-1.0.5.6.ebuild:
+ Version bumped.
+
+*texmacs-1.0.5.2 (29 May 2005)
+
+ 29 May 2005; Mamoru KOMACHI <usata@gentoo.org> +texmacs-1.0.5.2.ebuild:
+ Version bumped. This closes bug #94250.
+
+*texmacs-1.0.5 (21 May 2005)
+
+ 21 May 2005; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.4.4.ebuild,
+ -texmacs-1.0.4.5.ebuild, +texmacs-1.0.5.ebuild:
+ Version bumped. This closes bug #91064.
+
+*texmacs-1.0.4.7 (12 Apr 2005)
+
+ 12 Apr 2005; Mamoru KOMACHI <usata@gentoo.org> +texmacs-1.0.4.7.ebuild:
+ Version bumped.
+
+ 21 Feb 2005; Jan Brinkmann <luckyduck@gentoo.org> texmacs-1.0.4.5.ebuild:
+ added ~amd64 to KEYWORDS. fixes #71106
+
+ 02 Jan 2005; Ciaran McCreesh <ciaranm@gentoo.org> :
+ Change encoding to UTF-8 for GLEP 31 compliance
+
+ 11 Dec 2004; Jason Wever <weeve@gentoo.org> texmacs-1.0.4-r1.ebuild:
+ Stable on sparc.
+
+*texmacs-1.0.4.5 (11 Dec 2004)
+
+ 11 Dec 2004; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.4.3.ebuild,
+ +texmacs-1.0.4.5.ebuild:
+ Version bumped.
+
+*texmacs-1.0.4.4 (15 Nov 2004)
+
+ 15 Nov 2004; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.3-r1.ebuild,
+ +texmacs-1.0.4.4.ebuild, -texmacs-1.0.4.ebuild:
+ Version bumped. Added static USE flag. This closes bug #71195.
+
+ 04 Nov 2004; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.4-r1.ebuild,
+ -texmacs-1.0.4.1.ebuild:
+ Marked 1.0.4-r1 stable on x86, ppc and alpha.
+
+*texmacs-1.0.4.3 (10 Oct 2004)
+*texmacs-1.0.4-r1 (10 Oct 2004)
+
+ 10 Oct 2004; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.3.10.ebuild,
+ +texmacs-1.0.4-r1.ebuild, texmacs-1.0.4.1.ebuild, +texmacs-1.0.4.3.ebuild,
+ texmacs-1.0.4.ebuild:
+ Version bumped.
+
+*texmacs-1.0.4.1 (28 Aug 2004)
+
+ 28 Aug 2004; Mamoru KOMACHI <usata@gentoo.org> -texmacs-1.0.3.9.ebuild,
+ -texmacs-1.0.3.ebuild, +texmacs-1.0.4.1.ebuild, +texmacs-1.0.4.ebuild:
+ Version bumped. Removed old ebuilds.
+
+*texmacs-1.0.3.10 (07 Jul 2004)
+
+ 07 Jul 2004; Mamoru KOMACHI <usata@gentoo.org> +texmacs-1.0.3.10.ebuild,
+ -texmacs-1.0.3.7.ebuild:
+ Version bumped.
+
+*texmacs-1.0.3.9 (23 Jun 2004)
+
+ 23 Jun 2004; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.3-r1.ebuild,
+ +texmacs-1.0.3.9.ebuild, texmacs-1.0.3.ebuild:
+ Version bumped. Marked 1.0.3 stable.
+
+ 01 May 2004; Jason Wever <weeve@gentoo.org> texmacs-1.0.3.7.ebuild:
+ Added ~sparc keyword to help resolve #49540.
+
+ 26 Apr 2004; Bryan Østergaard <kloeri@gentoo.org> texmacs-1.0.3.7.ebuild:
+ Keyworded ~alpha, requested by Decade at freenode/#gentoo-alpha.
+
+*texmacs-1.0.3.7 (26 Apr 2004)
+*texmacs-1.0.3-r1 (26 Apr 2004)
+
+ 26 Apr 2004; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.1-r1.ebuild,
+ texmacs-1.0.2.4.ebuild, texmacs-1.0.3-r1.ebuild, texmacs-1.0.3.3.ebuild,
+ texmacs-1.0.3.7.ebuild, texmacs-1.0.3.ebuild:
+ Added ebuilds from stable and development branch. Marked 1.0.3
+ stable on x86. Added flag-o-matic back. (it is actually in portage
+ functions but it is recommended to inherit it)
+
+ 25 Apr 2004; Aron Griffis <agriffis@gentoo.org> texmacs-1.0.1-r1.ebuild:
+ Add die following econf for bug 48950
+
+*texmacs-1.0.3.3 (21 Feb 2004)
+*texmacs-1.0.3 (21 Feb 2004)
+
+ 12 Mar 2004; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.3.3.ebuild,
+ texmacs-1.0.3.ebuild, files/TeXmacs.desktop:
+ Added TeXmacs appliations menu entry, contributed by Keith Lea
+ <keith@cs.oswego.edu>. Closing bug #43545
+
+ 21 Feb 2004; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.1-r1.ebuild,
+ texmacs-1.0.1.23.ebuild, texmacs-1.0.1.ebuild, texmacs-1.0.2.4.ebuild,
+ texmacs-1.0.3.3.ebuild, texmacs-1.0.3.ebuild:
+ Version bumped, closing bug #38894. Removed old versions.
+
+ 09 Dec 2003; Heinrich Wendel <lanius@gentoo.org> texmacs-1.0.1-r1.ebuild,
+ texmacs-1.0.1.23.ebuild, texmacs-1.0.1.ebuild, texmacs-1.0.2.4.ebuild:
+ changed app-text/ghostscript to virtual/ghostscript
+
+*texmacs-1.0.2.4 (28 Oct 2003)
+
+ 28 Oct 2003; Mamoru KOMACHI <usata@gentoo.org> texmacs-1.0.1-r1.ebuild,
+ texmacs-1.0.1.23.ebuild, texmacs-1.0.1.ebuild, texmacs-1.0.2.4.ebuild:
+ Version bumped. Changed app-text/tetex to virtual/tetex.
+ Closing Bug #31032.
+
+ 14 Sep 2003; Mike Gardiner <obz@gentoo.org> texmacs-1.0.0.19.ebuild:
+ Removed old version
+
+*texmacs-1.0.1.23 (14 Sep 2003)
+
+ 14 Sep 2003; Mike Gardiner <obz@gentoo.org> texmacs-1.0.1.23.ebuild:
+ New version
+
+*texmacs-1.0.1-r1 (13 Sep 2003)
+
+ 13 Sep 2003; Mike Gardiner <obz@gentoo.org> texmacs-1.0.1-r1.ebuild:
+ New revision adding spell support through ispell
+
+ 12 Jun 2003; <msterret@gentoo.org> texmacs-1.0.0.19.ebuild,
+ texmacs-1.0.1.ebuild:
+ fix Header
+
+*texmacs-1.0.1 (02 Jan 2002)
+
+ 22 Apr 2003; Brandon Low <lostlogic@gentoo.org> texmacs-1.0.0.19.ebuild,
+ texmacs-1.0.1.ebuild:
+ Change supersed dependencies
+
+ 17 Mar 2003; Graham Forest <vladimir@gentoo.org> texmacs-1.0.1.ebuild:
+ set ~ppc in keywords
+
+ 02 Jan 2002; Matthew Turk <satai@gentoo.org> texmacs-1.0.1.ebuild :
+
+ Included some opts, manually turned off all inlining. Hopefully this'll work
+ nicely. Also bumped version.
+
+*texmacs-1.0.0.19 (23 Oct 2002)
+
+ 06 Nov 2002; Seemant Kulleen <seemant@gentoo.org> texmacs-1.0.0.19.ebuild :
+
+ Changed to use econf so things get installed in the correct locations
+ and custom CXXFLAGS settings. Closes bug #10220 by:
+ jap1@ionet.net (Jacob Perkins)
+
+ 23 Oct 2002; Matthew Turk <satai@gentoo.org> :
+
+ New version, testing. Changing to unstable.
+
+*texmacs-1.0.0.16 (13 Sep 2002)
+
+ 13 Sep 2002; Matthew Turk <satai@gentoo.org> ChangeLog :
+
+ New version, close submission #7860
+
+*texmacs-1.0.0.8 (03 Jul 2002)
+
+ 03 Jul 2002; Dan Armak <danarmak@gentoo.org> ChangeLog :
+
+ New version, close submission #4277
+
+*texmacs-1.0 (29 May 2002)
+
+ 29 May 2002; Dan Armak <danarmak@gentoo.org> changelog:
+
+ Initial ebuild. Based on bug #.
diff --git a/app-office/texmacs/Manifest b/app-office/texmacs/Manifest
new file mode 100644
index 000000000..0249f5e71
--- /dev/null
+++ b/app-office/texmacs/Manifest
@@ -0,0 +1,8 @@
+AUX TeXmacs.desktop 267 RMD160 9c538fb430c4e496a9571e84d0c1622c16279045 SHA1 baca78d1d4965ee4075158953a4c3fed26e855eb SHA256 f6292ac99e7adc8efd006df2dc458b4f8bc075dd5c4be2b8fdeb30a63198ff08
+AUX texmacs-maxima-5.14.0.patch 1591 RMD160 586582af7b7868a001f5891a70b7d4457beac055 SHA1 6979af5888ee29078667ec1b94e2164056cea8b7 SHA256 cb978cee2451c8a5a5405705aa114b024a54e0c66cd129f84d39ebd3a95cb29a
+DIST TeXmacs-1.0.6.12-src.tar.gz 4215464 RMD160 c1d53d8e20f0d701f1e2fb602753d7d85ae7fb53 SHA1 3fbddeb824703c61b5d4a193c4097f68305f9063 SHA256 7a90d5dd2a5d38753371dd37474034d361df019424f5c5b285b30c493adbe6a5
+DIST TeXmacs-600dpi-fonts.tar.gz 2899193 RMD160 b5a27a59ed0c178f94836b828d12d3534b506582 SHA1 0a3a279b842b63f55449856690483d07c6e1219c SHA256 e8eeb3c97a1405fd037b0567f683a6d2225d47c7829893b9768bd6c1c707cc81
+EBUILD texmacs-1.0.6.12-r1.ebuild 1639 RMD160 8a0491d6ae0195e04705814f435c237c8ef64422 SHA1 b7617eb66b6fd51b0209d7de3ca5b2327b6e6ce4 SHA256 88b4a29f99c1bc1bcd28f9ed6ee7d6af7c24392a34cb2eaddaadcba5d18e0ac3
+EBUILD texmacs-1.0.6.12.ebuild 1549 RMD160 c4a7557d529fddba1bf51b3390befbea09554249 SHA1 82a5cda34dde3cf6e4ae8f995bbfdea74ad0114f SHA256 abb5bf884d0b265582d0856418443f9a7471378fe927eb7c3fe639502db36312
+MISC ChangeLog 9768 RMD160 0ebc9161540b008e71248d53a62228c5340e6e0b SHA1 bf56ada7b6e8ff12fcc318b0d0174431d43c2672 SHA256 363da8509b46df2de78b5a219d0354ff0ddd980c851390ec96e80dedead4ef06
+MISC metadata.xml 447 RMD160 e29f6d98fb4ed38a56ef9415b5ce356f7660b8b5 SHA1 45c581010bad5fedc2ad5e2cb01722e51b618269 SHA256 65665d792841d785709329fb8d2770006cc9888a992b0ce64f5572f4b25520ab
diff --git a/app-office/texmacs/files/TeXmacs.desktop b/app-office/texmacs/files/TeXmacs.desktop
new file mode 100644
index 000000000..f51ffe604
--- /dev/null
+++ b/app-office/texmacs/files/TeXmacs.desktop
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Encoding=UTF-8
+Version=1.0
+Type=Application
+Exec=texmacs
+Icon=/usr/share/TeXmacs/misc/pixmaps/TeXmacs.xpm
+Name=TeXmacs
+GenericName=Scientific Word Processor
+Comment=A scientific word processing application.
+Categories=Application;Office;WordProcessor
diff --git a/app-office/texmacs/files/texmacs-maxima-5.14.0.patch b/app-office/texmacs/files/texmacs-maxima-5.14.0.patch
new file mode 100644
index 000000000..0281cf9bf
--- /dev/null
+++ b/app-office/texmacs/files/texmacs-maxima-5.14.0.patch
@@ -0,0 +1,24 @@
+diff -U2 --recursive TeXmacs-1.0.6.12-src-orig/plugins/maxima/bin/maxima_detect TeXmacs-1.0.6.12-src/plugins/maxima/bin/maxima_detect
+--- TeXmacs-1.0.6.12-src-orig/plugins/maxima/bin/maxima_detect 2007-11-05 15:21:32.000000000 +0600
++++ TeXmacs-1.0.6.12-src/plugins/maxima/bin/maxima_detect 2008-01-09 04:43:10.000000000 +0600
+@@ -63,7 +63,8 @@
+ version 5.11
+ version 5.12
+-version 5.13" >/dev/null
++version 5.13
++version 5.14" >/dev/null
+ then
+- # 5.9.1 or 5.9.2 or 5.9.3 or 5.10 or 5.11 or 5.12 or 5.13
++ # 5.9.1 or 5.9.2 or 5.9.3 or 5.10 or 5.11 or 5.12 or 5.13 or 5.14
+ maxima -d | grep -F 'maxima-htmldir=' | sed -e \
+ 's/maxima-htmldir=/"/' -e 's|$|/maxima_toc.html"|'
+diff -U2 --recursive TeXmacs-1.0.6.12-src-orig/plugins/maxima/bin/tm_maxima TeXmacs-1.0.6.12-src/plugins/maxima/bin/tm_maxima
+--- TeXmacs-1.0.6.12-src-orig/plugins/maxima/bin/tm_maxima 2007-11-05 15:21:32.000000000 +0600
++++ TeXmacs-1.0.6.12-src/plugins/maxima/bin/tm_maxima 2008-01-09 04:43:10.000000000 +0600
+@@ -18,5 +18,5 @@
+ 5.9.1.1* | 5.9.2* | 5.9.3*) exec maxima -u $1 -l $2 -p "$TEXMACS_MAXIMA_PATH/texmacs-maxima-5.9.2.lisp";;
+ 5.10.*) exec maxima -u $1 -l $2 -p "$TEXMACS_MAXIMA_PATH/texmacs-maxima-5.10.0.lisp";;
+- 5.11.* | 5.12.* | 5.13.*) exec maxima -u $1 -l $2 -p "$TEXMACS_MAXIMA_PATH/texmacs-maxima-5.11.0.lisp";;
++ 5.11.* | 5.12.* | 5.13.* | 5.14.*) exec maxima -u $1 -l $2 -p "$TEXMACS_MAXIMA_PATH/texmacs-maxima-5.11.0.lisp";;
+ cygwin)
+ exec maxima.bat -p "`echo $TEXMACS_MAXIMA_PATH/texmacs-maxima-5.11.0.lisp|cygpath --windows -f -`";;
diff --git a/app-office/texmacs/metadata.xml b/app-office/texmacs/metadata.xml
new file mode 100644
index 000000000..849d5af06
--- /dev/null
+++ b/app-office/texmacs/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>text-markup</herd>
+<longdescription lang="en">
+GNU TeXmacs is a WYSIWYG text processor with an excellent quality
+of both texts and mathematical formulae. It can import and export
+LaTeX and html. It is used as a GUI for a number of computer algebra
+and numerical mathematics systems.
+</longdescription>
+</pkgmetadata>
diff --git a/app-office/texmacs/texmacs-1.0.6.12-r1.ebuild b/app-office/texmacs/texmacs-1.0.6.12-r1.ebuild
new file mode 100644
index 000000000..087821715
--- /dev/null
+++ b/app-office/texmacs/texmacs-1.0.6.12-r1.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+inherit eutils
+MY_P=${P/tex/TeX}-src
+DESCRIPTION="Wysiwyg text processor with high-quality maths"
+
+SRC_URI="ftp://ftp.texmacs.org/pub/TeXmacs/targz/${MY_P}.tar.gz
+ ftp://ftp.texmacs.org/pub/TeXmacs/targz/TeXmacs-600dpi-fonts.tar.gz"
+
+HOMEPAGE="http://www.texmacs.org/"
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="imlib jpeg svg netpbm spell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="virtual/latex-base
+ virtual/ghostscript
+ >=dev-scheme/guile-1.4
+ media-libs/freetype
+ x11-libs/libXext
+ imlib? ( media-libs/imlib2 )
+ jpeg? ( || ( media-gfx/imagemagick media-gfx/jpeg2ps ) )
+ svg? ( || ( media-gfx/inkscape gnome-base/librsvg ) )
+ netpbm? ( media-libs/netpbm )
+ spell? ( || ( >=app-text/ispell-3.2 >=app-text/aspell-0.5 ) )"
+
+DEPEND="${RDEPEND}
+ x11-proto/xproto"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+ if has_version ">=dev-scheme/guile-1.8"; then
+ if ! built_with_use dev-scheme/guile deprecated; then
+ eerror "Please re-emerge dev-scheme/guile with the USE flag +deprecated"
+ die "Bad guile version"
+ fi
+ fi
+}
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${PN}-maxima-5.14.0.patch
+}
+
+src_compile() {
+ econf $(use_with imlib imlib2 ) \
+ --enable-optimize="${CXXFLAGS}" \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc TODO || die "dodoc failed"
+ domenu "${FILESDIR}/TeXmacs.desktop" || die "domenu failed"
+
+ # now install the fonts
+ insinto /usr/share/texmf
+ doins -r "${WORKDIR}/fonts" || die "installing fonts failed"
+}
diff --git a/app-office/texmacs/texmacs-1.0.6.12.ebuild b/app-office/texmacs/texmacs-1.0.6.12.ebuild
new file mode 100644
index 000000000..6313874f5
--- /dev/null
+++ b/app-office/texmacs/texmacs-1.0.6.12.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+inherit eutils
+MY_P=${P/tex/TeX}-src
+DESCRIPTION="Wysiwyg text processor with high-quality maths"
+
+SRC_URI="ftp://ftp.texmacs.org/pub/TeXmacs/targz/${MY_P}.tar.gz
+ ftp://ftp.texmacs.org/pub/TeXmacs/targz/TeXmacs-600dpi-fonts.tar.gz"
+
+HOMEPAGE="http://www.texmacs.org/"
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="imlib jpeg svg netpbm spell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="virtual/latex-base
+ virtual/ghostscript
+ >=dev-scheme/guile-1.4
+ media-libs/freetype
+ x11-libs/libXext
+ imlib? ( media-libs/imlib2 )
+ jpeg? ( || ( media-gfx/imagemagick media-gfx/jpeg2ps ) )
+ svg? ( || ( media-gfx/inkscape gnome-base/librsvg ) )
+ netpbm? ( media-libs/netpbm )
+ spell? ( || ( >=app-text/ispell-3.2 >=app-text/aspell-0.5 ) )"
+
+DEPEND="${RDEPEND}
+ x11-proto/xproto"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+ if has_version ">=dev-scheme/guile-1.8"; then
+ if ! built_with_use dev-scheme/guile deprecated; then
+ eerror "Please re-emerge dev-scheme/guile with the USE flag +deprecated"
+ die "Bad guile version"
+ fi
+ fi
+}
+
+src_compile() {
+ econf $(use_with imlib imlib2 ) \
+ --enable-optimize="${CXXFLAGS}" \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc TODO || die "dodoc failed"
+ domenu "${FILESDIR}/TeXmacs.desktop" || die "domenu failed"
+
+ # now install the fonts
+ insinto /usr/share/texmf
+ doins -r "${WORKDIR}/fonts" || die "installing fonts failed"
+}
diff --git a/dev-cpp/growler-arch/ChangeLog b/dev-cpp/growler-arch/ChangeLog
new file mode 100644
index 000000000..3549c930f
--- /dev/null
+++ b/dev-cpp/growler-arch/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for dev-cpp/growler-arch
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 04 Nov 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ version bump
+ growler-arch-0.3.7.1: added
+
+ 31 Oct 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ removed CRs from DESCRIPTION
+
+*growler-arch-0.3.7 (28 Oct 2007)
+
+ 28 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-arch-0.3.7.ebuild:
+ Initial import
+
diff --git a/dev-cpp/growler-arch/Manifest b/dev-cpp/growler-arch/Manifest
new file mode 100644
index 000000000..d3a7285d4
--- /dev/null
+++ b/dev-cpp/growler-arch/Manifest
@@ -0,0 +1,6 @@
+DIST growler-arch-0.3.7.1.tar.gz 500709 RMD160 75eab31464ed4de9125f7dac6b2946d918c7b15a SHA1 c5b50bd795ea788f00ccc68e9a65cfa31eaa5c3f SHA256 36b53a1ac6eb4602c4a20b430c9f81db3e6ed442d7df1ea35f636367eb29f634
+DIST growler-arch-0.3.7.tar.gz 504370 RMD160 5554b0987f7fffc126b3af8a04fd8d00d3274ec3 SHA1 e99bf6fdcbf9b50f7529a8ce451fa918072ff7ba SHA256 385e6045e8f5d6a85ab98c00d84fcf772bf554ab48a6566bba84a357b342565d
+EBUILD growler-arch-0.3.7.1.ebuild 881 RMD160 fd7dfedb2602195524816f17c63a86c632102c6c SHA1 ddf76fbf6d1f1b62f5a0d62402ce6621ae8535cb SHA256 3912f2b1c455e2eb22e842381023b9ac4d5860239e5fafdd09e528f68ea3e37a
+EBUILD growler-arch-0.3.7.ebuild 881 RMD160 fd7dfedb2602195524816f17c63a86c632102c6c SHA1 ddf76fbf6d1f1b62f5a0d62402ce6621ae8535cb SHA256 3912f2b1c455e2eb22e842381023b9ac4d5860239e5fafdd09e528f68ea3e37a
+MISC ChangeLog 460 RMD160 21b4058f7a9a2ac74643b5bdef9debb554eab239 SHA1 f5454a9a59889f6fabd14d94735a764ed6cf1d5e SHA256 3067ac62ed24199a56163b3d14b73d6e1df48cdfbc1d303e2217db31d0dd2327
+MISC metadata.xml 403 RMD160 eb11eed8d86814a3bc18c6185289d7c129bfa1d6 SHA1 b630e3bd275e92baf5e5f4ba9f7846c94e76a823 SHA256 0d8401b8acb7994b11d81d48fbba30b26e180f4b14e585e922d3e9ab653125c5
diff --git a/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild b/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild
new file mode 100644
index 000000000..094704766
--- /dev/null
+++ b/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Arch is the set growler libraries and utilities that provide a distributed object architecture and environment."
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-arch-${PV}.tar.gz"
+
+IUSE="doc static"
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7
+ >=dev-cpp/growler-thread-0.3.4
+ >=dev-cpp/growler-core-0.3.7"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen dev-libs/libxslt )"
+
+src_compile() {
+ econf \
+ $(use_enable doc) \
+ $(use_enable static) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-arch/growler-arch-0.3.7.ebuild b/dev-cpp/growler-arch/growler-arch-0.3.7.ebuild
new file mode 100644
index 000000000..094704766
--- /dev/null
+++ b/dev-cpp/growler-arch/growler-arch-0.3.7.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Arch is the set growler libraries and utilities that provide a distributed object architecture and environment."
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-arch-${PV}.tar.gz"
+
+IUSE="doc static"
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7
+ >=dev-cpp/growler-thread-0.3.4
+ >=dev-cpp/growler-core-0.3.7"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen dev-libs/libxslt )"
+
+src_compile() {
+ econf \
+ $(use_enable doc) \
+ $(use_enable static) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-arch/metadata.xml b/dev-cpp/growler-arch/metadata.xml
new file mode 100644
index 000000000..6ead47f4b
--- /dev/null
+++ b/dev-cpp/growler-arch/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bryan.d.green@nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler-Arch is the set growler libraries and utilities that provide a
+distributed object architecture and environment.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-cpp/growler-core/ChangeLog b/dev-cpp/growler-core/ChangeLog
new file mode 100644
index 000000000..03a66ce6f
--- /dev/null
+++ b/dev-cpp/growler-core/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for dev-cpp/growler-core
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 31 Oct 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ removed CRs from DESCRIPTION
+
+*growler-core-0.3.7 (28 Oct 2007)
+
+ 28 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-core-0.3.7.ebuild:
+ Initial import
+
diff --git a/dev-cpp/growler-core/Manifest b/dev-cpp/growler-core/Manifest
new file mode 100644
index 000000000..52dda3ce7
--- /dev/null
+++ b/dev-cpp/growler-core/Manifest
@@ -0,0 +1,4 @@
+DIST growler-core-0.3.7.tar.gz 271855 RMD160 b488a484710ed8d51e7b715c8b768b16aaa18ea6 SHA1 c4b5204fece1c410c0d3f1a9a74a5eb655599a6b SHA256 f71b42d657276590538f9f737bb97b4a0a625987e37d3d2584d4d137fefbcae9
+EBUILD growler-core-0.3.7.ebuild 994 RMD160 9b3ff1cd0a13a24454a35534f9adf6592cfbb3c3 SHA1 36740bc29e33e75f9590a1e33e0808b994c93575 SHA256 e3916f63cea31eff635d98e96eee6c3652557261a6abfcf9cccb66d2a0936bbe
+MISC ChangeLog 351 RMD160 31a4a677675ed926c55c05213559e295bcd72633 SHA1 5b33d2b0d8d43f698fd74e0ca7d0c72e47c8126b SHA256 af441ed505ca7e985bda26aa30d63c1cf2b153e3bb4aa89e63389e1e7373cf8e
+MISC metadata.xml 442 RMD160 3392fe65e2130d30032dbf246f8532d03b096bbb SHA1 1f03f148118e5c8150d5a38f84b30a93ad55ce44 SHA256 1ca2a6d3ea5bf266cfb1013704b6d01e73ff2a1bf9053bb6fd9a35f35af18925
diff --git a/dev-cpp/growler-core/growler-core-0.3.7.ebuild b/dev-cpp/growler-core/growler-core-0.3.7.ebuild
new file mode 100644
index 000000000..ed85818c3
--- /dev/null
+++ b/dev-cpp/growler-core/growler-core-0.3.7.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /CVS/groups/vistech/bgreen-overlay/dev-cpp/growler-core/growler-core-0.3.1.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Core provides a large set of mainly general-purpose classes and functionality for developing and using the Growler Distributed Component Architecture."
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-core-${PV}.tar.gz"
+
+IUSE="doc static"
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7
+ >=dev-cpp/growler-thread-0.3.4"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_compile() {
+ econf \
+ $(use_enable doc) \
+ $(use_enable static) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-core/metadata.xml b/dev-cpp/growler-core/metadata.xml
new file mode 100644
index 000000000..64e9f0940
--- /dev/null
+++ b/dev-cpp/growler-core/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bryan.d.green@nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler-Core provides a large set of mainly general-purpose classes and
+functionality for developing and using the Growler Distributed Component
+Architecture.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-cpp/growler-link/ChangeLog b/dev-cpp/growler-link/ChangeLog
new file mode 100644
index 000000000..7212b1489
--- /dev/null
+++ b/dev-cpp/growler-link/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for dev-cpp/growler-link
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 31 Oct 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ removed CRs from DESCRIPTION
+
+*growler-link-0.3.7 (28 Oct 2007)
+
+ 28 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-link-0.3.7.ebuild: Initial import
+
diff --git a/dev-cpp/growler-link/Manifest b/dev-cpp/growler-link/Manifest
new file mode 100644
index 000000000..4fedf2591
--- /dev/null
+++ b/dev-cpp/growler-link/Manifest
@@ -0,0 +1,4 @@
+DIST growler-link-0.3.7.tar.gz 548768 RMD160 38153300e2ea8375116804ffe3823e0fabd3a831 SHA1 9384b97e7d9010d4a85c8cfbc26f71f312520943 SHA256 eec2e6f91146bc68004114adc7ee00617eab4b459649029cfcdcfc4db3d17719
+EBUILD growler-link-0.3.7.ebuild 996 RMD160 b54fe7584ff7e33f55d45b9c42747eed7b92c451 SHA1 a6eff71afbd79a7e60576aee68d6aa568faa67e0 SHA256 fc0275e210207dfe224b7f8df0d00990ff711bdfd100ad6db166f53a65a2e0f8
+MISC ChangeLog 349 RMD160 2d40156198544a346bea4e83b1a31615f5c77aa0 SHA1 a3d96a6fb1bbd0e51a50231dcebc25f35761cf3d SHA256 2237f8162fe35e86fb21f6e39f9d93786d7567fb2f4f754ce643e0f1d1205b33
+MISC metadata.xml 481 RMD160 be4b7a9b4472d0c3861813d9f8f3097a00e9577e SHA1 ea067e55e4948b6015acc9c08e3df412ea2c0b12 SHA256 79b99b68b79b06620061d066e89197fff4f24f8b6c8a559bca2d0b6c20752e24
diff --git a/dev-cpp/growler-link/growler-link-0.3.7.ebuild b/dev-cpp/growler-link/growler-link-0.3.7.ebuild
new file mode 100644
index 000000000..01be8cafe
--- /dev/null
+++ b/dev-cpp/growler-link/growler-link-0.3.7.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /CVS/groups/vistech/bgreen-overlay/dev-cpp/growler-link/growler-link-0.3.1.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Link: the lowest-level Growler library. Support for dynamic linking, components, logging, etc."
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-link-${PV}.tar.gz"
+
+IUSE="doc tcpd static fortran"
+
+RDEPEND=">=dev-libs/boost-1.33.1
+ tcpd? ( sys-apps/tcp-wrappers )"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_compile() {
+ econf \
+ $(use_enable doc) \
+ $(use_enable tcpd) \
+ $(use_enable static) \
+ $(use_enable fortran) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-link/metadata.xml b/dev-cpp/growler-link/metadata.xml
new file mode 100644
index 000000000..219475162
--- /dev/null
+++ b/dev-cpp/growler-link/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bryan.d.green@nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler-Link is the lowest-level Growler package. It provides basic support for
+dynamic linking, components and modules, as well as several other of Growler's
+commonly used API's, such as Clogger.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-cpp/growler-math/ChangeLog b/dev-cpp/growler-math/ChangeLog
new file mode 100644
index 000000000..4b412fb6b
--- /dev/null
+++ b/dev-cpp/growler-math/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for dev-cpp/growler-math
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*growler-math-0.3.4 (28 Oct 2007)
+
+ 24 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-math-0.3.4.ebuild:
+ Initial import
+
diff --git a/dev-cpp/growler-math/Manifest b/dev-cpp/growler-math/Manifest
new file mode 100644
index 000000000..792e16f52
--- /dev/null
+++ b/dev-cpp/growler-math/Manifest
@@ -0,0 +1,4 @@
+DIST growler-math-0.3.4.1.tar.gz 178883 RMD160 961c086126a015cce4376250e1ccb8dcccbc664c SHA1 78012b37e10b2c1069e0d185c8c1ffb4184c7a3f SHA256 ba578c958fab839a668ac8c00c27b5724ef5e0fd4e0e65bb45ef74d7603c4163
+EBUILD growler-math-0.3.4.1.ebuild 818 RMD160 8596276d58564acc17cac042f457222f87868a3e SHA1 435d3517ffc5147ead704e9c4b54d074326ba9a8 SHA256 fe856244a0acc1302bcadb81e7b8e10b2f70c55eccff0831f9287bfdd2237f73
+MISC ChangeLog 256 RMD160 547bae9bb091d79d96821de721c2b18019382ba9 SHA1 4a950914596efa91c761b786a4e807cd261ee6ef SHA256 f5d3f343281fd2dbb2773238e05a9859ff7a089b4dcc828e3bf1d90c7400d574
+MISC metadata.xml 350 RMD160 488715a22626bdf0d3d471abea8fe140a4989232 SHA1 dc4faad6c9b64ee78a652920fe502aa462303a97 SHA256 a86812515d51878f98ac712d799c5143cd0230d10d2767c9c3c18add75ce553c
diff --git a/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild b/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild
new file mode 100644
index 000000000..cea8c5f21
--- /dev/null
+++ b/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /CVS/groups/vistech/bgreen-overlay/dev-cpp/growler-math/growler-math-0.3.1.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Math provides a set of math-related classes and functionality"
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-math-${PV}.tar.gz"
+
+IUSE="static"
+
+RDEPEND=">=dev-cpp/growler-core-0.3.7"
+
+DEPEND="${RDEPEND}"
+
+src_compile() {
+ econf \
+ $(use_enable static) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-math/metadata.xml b/dev-cpp/growler-math/metadata.xml
new file mode 100644
index 000000000..4a36e329d
--- /dev/null
+++ b/dev-cpp/growler-math/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bgreen@nas.nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler-Math provides a set of math-related classes and functionality
+</longdescription>
+</pkgmetadata>
diff --git a/dev-cpp/growler-thread/ChangeLog b/dev-cpp/growler-thread/ChangeLog
new file mode 100644
index 000000000..6f5491e07
--- /dev/null
+++ b/dev-cpp/growler-thread/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for dev-cpp/growler-thread
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 31 Oct 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ removed CRs from DESCRIPTION
+
+*growler-thread-0.3.4 (28 Oct 2007)
+
+ 28 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-thread-0.3.4.ebuild:
+ Initial import
+
diff --git a/dev-cpp/growler-thread/Manifest b/dev-cpp/growler-thread/Manifest
new file mode 100644
index 000000000..67b118aae
--- /dev/null
+++ b/dev-cpp/growler-thread/Manifest
@@ -0,0 +1,4 @@
+DIST growler-thread-0.3.4.tar.gz 183150 RMD160 fcae2988a68af50b3bda0982658ad301eb990f8e SHA1 96697ae8931427cc8b47717e1d43199359fade3d SHA256 9749203246608dca2172d80a11a54ff80846f909b54e9f0fdea960413fdd11ca
+EBUILD growler-thread-0.3.4.ebuild 932 RMD160 98f39d2a430ddb6a17f5b2eac07eeee42c60785a SHA1 491581a609423bfad706a40897cf352e1df495cc SHA256 6df2b86b6cd54cc877518cd4effe0f13660fe35d6657c98b84917929b7d734d8
+MISC ChangeLog 357 RMD160 54c356304403b8360a77caf6cadf11100ebd3390 SHA1 94150a2ea4025d9fa4257bee9dcab552a6b45487 SHA256 f283c9e46c83ebc1746ff5f284965c249faa3f3b6acba9c4821dce6096ed979d
+MISC metadata.xml 424 RMD160 87b5e9b5d812b13051a4176f28624be8d52fd645 SHA1 8ec143607a49a7c20edb483f9fc31717aea45e56 SHA256 3f1b7dbdd2ab5fc20e02b3461b7022b3e604930eff8943f9c8f74ac58f1af7ec
diff --git a/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild b/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild
new file mode 100644
index 000000000..2d4793be7
--- /dev/null
+++ b/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /CVS/groups/vistech/bgreen-overlay/dev-cpp/growler-thread/growler-thread-0.3.1.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler-Thread is a pthread wrapper library. It provides support for creating threads, and for common multithreading tasks."
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+SRC_URI="${HOMEPAGE}/downloads/growler-thread-${PV}.tar.gz"
+
+IUSE="doc static"
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_compile() {
+ econf \
+ $(use_enable doc) \
+ $(use_enable static) \
+ --enable-fast-install \
+ || die "could not configure"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc README NEWS AUTHORS NOSA ChangeLog
+}
+
diff --git a/dev-cpp/growler-thread/metadata.xml b/dev-cpp/growler-thread/metadata.xml
new file mode 100644
index 000000000..3d0e96364
--- /dev/null
+++ b/dev-cpp/growler-thread/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bryan.d.green@nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler-Thread is a pthread wrapper library used by Growler. It provides
+support for creating threads, and for common multithreading tasks.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-cpp/growler/ChangeLog b/dev-cpp/growler/ChangeLog
new file mode 100644
index 000000000..e733b47fa
--- /dev/null
+++ b/dev-cpp/growler/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for dev-cpp/growler
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*growler-0.3.8 (28 Oct 2007)
+
+ 24 Oct 2007; Bryan Green <bryan.d.green@nasa.gov>
+ +growler-0.3.8.ebuild:
+ Initial import
+
diff --git a/dev-cpp/growler/Manifest b/dev-cpp/growler/Manifest
new file mode 100644
index 000000000..8b9d1bd55
--- /dev/null
+++ b/dev-cpp/growler/Manifest
@@ -0,0 +1,4 @@
+EBUILD growler-0.3.8.2.ebuild 516 RMD160 0cfd1bcdcc2050eb13a138b5f15a00b85dbdde06 SHA1 5a529a719accbf2e3c914e9e10191c163cdad3fa SHA256 4a1f438b168e7ba000744a574c29d00167c7e212f0374ac27c67725090a853aa
+EBUILD growler-0.3.8.ebuild 514 RMD160 e36ed5902ff23d3e125532643f9a4586db1ee934 SHA1 f8f1c36112f3cea98de05b7b99ceb82e5f29bb85 SHA256 87d67fee9025cca6394cf416b5fc1aea0600d48670ed91027f13fa7d17fb4d9c
+MISC ChangeLog 241 RMD160 66c5f532275259f57c9b87faae57d771bfb3102b SHA1 bbd56cdbadb96c1f059ec205e582142c32a28a72 SHA256 5ca35c1e86e137f2c5a5bd70938469bb842254cdf0697287e73720ebe7fad62f
+MISC metadata.xml 349 RMD160 8d5660240cfed2145b21c55ab3f1b157841cadcc SHA1 8a87a194f1f8e8bbc8f4f82d006ff663fe003b44 SHA256 827f565545ee7e4886535c0902fe83bf05883c64e54fce9d2615c5da9b49bd42
diff --git a/dev-cpp/growler/growler-0.3.8.2.ebuild b/dev-cpp/growler/growler-0.3.8.2.ebuild
new file mode 100644
index 000000000..2e6b48c6c
--- /dev/null
+++ b/dev-cpp/growler/growler-0.3.8.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler is a set of libraries and utilities that
+provide a distributed object architecture and environment."
+
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+
+IUSE=""
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7
+ >=dev-cpp/growler-thread-0.3.4
+ >=dev-cpp/growler-core-0.3.7
+ >=dev-cpp/growler-arch-0.3.7.1"
+
+DEPEND="${RDEPEND}"
+
diff --git a/dev-cpp/growler/growler-0.3.8.ebuild b/dev-cpp/growler/growler-0.3.8.ebuild
new file mode 100644
index 000000000..ed27e234d
--- /dev/null
+++ b/dev-cpp/growler/growler-0.3.8.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+SLOT="0"
+LICENSE="NOSA"
+
+KEYWORDS="~amd64 ~x86"
+
+DESCRIPTION="Growler is a set of libraries and utilities that
+provide a distributed object architecture and environment."
+
+HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
+
+IUSE=""
+
+RDEPEND=">=dev-cpp/growler-link-0.3.7
+ >=dev-cpp/growler-thread-0.3.4
+ >=dev-cpp/growler-core-0.3.7
+ >=dev-cpp/growler-arch-0.3.7"
+
+DEPEND="${RDEPEND}"
+
diff --git a/dev-cpp/growler/metadata.xml b/dev-cpp/growler/metadata.xml
new file mode 100644
index 000000000..9a5998677
--- /dev/null
+++ b/dev-cpp/growler/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cpp</herd>
+<maintainer>
+<email>bryan.d.green@nasa.gov</email>
+<name>Bryan Green</name>
+</maintainer>
+<longdescription>
+Growler is a C++-based distributed object and event architecture.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-lang/aldor/ChangeLog b/dev-lang/aldor/ChangeLog
new file mode 100644
index 000000000..5e3c7005c
--- /dev/null
+++ b/dev-lang/aldor/ChangeLog
@@ -0,0 +1,22 @@
+# ChangeLog for sci-mathematics/yorick
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*aldor-1.1.0 (09 Oct 2007)
+
+ 09 Oct 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +aldor-1.1.0.ebuild +files/aldor-1.1.0.patch
+ -aldor-1.0.3.ebuild -aldor-1.1.0_rc.ebuild:
+ The first opensource release!
+
+*aldor-1.1.0_rc (20 Apr 2007)
+
+ 20 Apr 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +aldor-1.1.0_rc.ebuild:
+ Version bump
+
+*aldor-1.0.3 (15 Feb 2007)
+
+ 15 Feb 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +metadata.xml, +aldor-1.0.3.ebuild:
+ Initial import, bug 131590
diff --git a/dev-lang/aldor/Manifest b/dev-lang/aldor/Manifest
new file mode 100644
index 000000000..6c2cf04db
--- /dev/null
+++ b/dev-lang/aldor/Manifest
@@ -0,0 +1,9 @@
+AUX aldor-1.1.0.patch 837 RMD160 e43ce6c6e17c43bc2a8223e85dcaed70c3a482fb SHA1 0daa89ff91aac843c95f864636534e9eb29f0014 SHA256 dee4048e8fc96d2a675bbedb17998210c4b1cb95035e0d4beaabd1af8038e7e0
+DIST aldor.el.nw 51482 RMD160 8b785abf23ea5cd1107d1a05b187723f81b04559 SHA1 628ff6f36d720e4a32d72125d3559e4da498f750 SHA256 c6c80e1fd32b36555fe3d90e9cadb48795907514129b6c23406f720db18bd43e
+DIST aldorug.pdf.gz 767850 RMD160 7b2f9496b303caee0642ea74e58524699b122f19 SHA1 02e89472a34fe974900a529c644c093c55452793 SHA256 dec98eed7c9065c9233d2eb3e30e5dc98a2128709d541f7b626d086979b80c3a
+DIST algebra.html.tar.gz 749742 RMD160 9b0d1d2a7d7cda047a911ee9d2f1a23d21ed6b76 SHA1 8cf0853897947b7f073ff62efda6b14ec8edf7f2 SHA256 b4e38a1d36e4f4661df0314da43aa09846e6c62156ac4243bcb051dcc829e33f
+DIST libaldor.pdf.gz 434487 RMD160 c7d7130eca8d820a291786f11288deefbe1a672e SHA1 e231e2171b5906ba0812508d548c759f235625b5 SHA256 57371d1bd6031c350783e063533ba9ba1d82e681dca54fa3b4de42a339c9a668
+DIST tutorial.pdf.gz 164786 RMD160 1ceea46bd6a7b22003ff06842d656b0d57d011bf SHA1 62a4d224a60b6abc1fc8d49ac0f2a41860f001da SHA256 a0339b7c59632c8825e26603330b5a4010aeeb843ddad06c6b54d029519c7e65
+EBUILD aldor-1.1.0.ebuild 2183 RMD160 e4f736d6b44b66f9766b1cb5bc161654f06ba7c0 SHA1 843d29cffabd9918fe00139afce5436fc891af5a SHA256 82715caea0cca00737a6b2b1b1322a8d49d66c9d6aaa6538a97ccb1349bcb62f
+MISC ChangeLog 604 RMD160 0e82b957c36f50bc4f1ea826dc11b9507f9e3fc3 SHA1 3f1237a0ad448efa3d3324eaa19f1f1567732074 SHA256 c1874a2da1126c705e8a31098c6c7c12bec8c2f101bd35a353fafe770bc3db15
+MISC metadata.xml 811 RMD160 f7b329f9abd26f80f54235f2ad214bd4d8fd6d92 SHA1 e95d400caa56b900562d16d943ab8da837c281ed SHA256 005c18ae92ac4022daa3da7381a2eb712c28b6444f853c1a889cbc4750d8f9ef
diff --git a/dev-lang/aldor/aldor-1.1.0.ebuild b/dev-lang/aldor/aldor-1.1.0.ebuild
new file mode 100644
index 000000000..3f5e90a1f
--- /dev/null
+++ b/dev-lang/aldor/aldor-1.1.0.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+inherit subversion elisp-common
+
+DESCRIPTION="Aldor - programming language with a two-level type system"
+HOMEPAGE="http://www.aldor.org/"
+LICENSE="aldor-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="doc emacs"
+RDEPEND="emacs? ( virtual/emacs )"
+DEPEND="${RDEPEND}
+ dev-util/byacc
+ emacs? ( app-text/noweb doc? ( virtual/tetex ) )"
+ESVN_REPO_URI="https://aquarium.aldor.csd.uwo.ca/svn/trunk"
+SRC_URI="doc? ( http://aldor.org/docs/aldorug.pdf.gz
+ http://aldor.org/docs/libaldor.pdf.gz
+ http://aldor.org/docs/tutorial.pdf.gz
+ ftp://ftp-sop.inria.fr/cafe/software/algebra/algebra.html.tar.gz )
+ emacs? ( http://www.risc.uni-linz.ac.at/people/hemmecke/aldor/aldor.el.nw )"
+
+src_compile() {
+ if use emacs; then
+ einfo "The aldor emacs mode"
+ notangle "${DISTDIR}/aldor.el.nw" > aldor.el
+ notangle -Rinit.el "${DISTDIR}/aldor.el.nw" | \
+ sed -e '1s/^.*$/;; aldor mode/' > 64aldor-gentoo.el
+ if use doc; then
+ einfo "Documentation for the aldor emacs mode"
+ noweave "${DISTDIR}/aldor.el.nw" > aldor-mode.tex
+ pdflatex aldor-mode.tex
+ pdflatex aldor-mode.tex
+ fi
+ fi
+ if use doc; then
+ einfo "Documentation"
+ cp "${DISTDIR}/aldorug.pdf.gz" .
+ cp "${DISTDIR}/libaldor.pdf.gz" .
+ cp "${DISTDIR}/tutorial.pdf.gz" .
+ gunzip aldorug.pdf.gz libaldor.pdf.gz tutorial.pdf.gz
+ tar xzf "${DISTDIR}/algebra.html.tar.gz"
+ fi
+ cd "${PN}"
+ einfo "Compiling aldor and its libraries"
+ epatch "${FILESDIR}/${P}.patch"
+ emake distrib
+}
+
+src_install() {
+ cd "${S}"
+ cat > 64aldor <<EOF
+ALDORROOT=/opt/${PN}/linux/${PV}
+PATH=/opt/${PN}/linux/${PV}/bin
+EOF
+ doenvd 64aldor
+ if use doc; then
+ einfo "Installing the aldor documentation"
+ insinto "/usr/share/doc/${P}"
+ doins *.pdf
+ doins -r algebra.html
+ fi
+ if use emacs; then
+ einfo "Installing the aldor emacs mode"
+ elisp-site-file-install aldor.el
+ elisp-site-file-install 64aldor-gentoo.el
+ fi
+ einfo "Installing aldor and its libraries"
+ cd "${PN}/install"
+ dodir /opt
+ cp -a "${PN}" "${D}opt/"
+}
+
+pkg_postinst() {
+ use emacs && elisp-site-regen
+}
+
+pkg_prerm() {
+ [ -f "${SITELISP}/site-gentoo.el" ] && elisp-site-regen
+}
diff --git a/dev-lang/aldor/files/aldor-1.1.0.patch b/dev-lang/aldor/files/aldor-1.1.0.patch
new file mode 100644
index 000000000..e1807e44e
--- /dev/null
+++ b/dev-lang/aldor/files/aldor-1.1.0.patch
@@ -0,0 +1,23 @@
+--- Makefile.globals.orig 2007-09-30 22:59:31.000000000 +0700
++++ Makefile.globals 2007-09-30 22:57:27.000000000 +0700
+@@ -21,5 +21,5 @@
+ #
+ SHELL=/bin/bash
+-ALDOR_PROJECT=d:\projects\aldor\aldorsvn
++ALDOR_PROJECT=$(S)/$(PN)
+
+ # All these things under $(ALDOR_PROJECT) can actually be in unrelated places,
+@@ -33,5 +33,5 @@
+ # MACHINE should be one of: linux, win32gcc, win32msvc, sun4os55g64
+ # or the machines listed in: $(ALDOR_PROJECT)/aldor/tools/unix/docc.
+-MACHINE=win32msvc
++MACHINE=linux
+
+ # This varible sets the name of the libraries to be built
+@@ -43,5 +43,5 @@
+ # Note: the order in the list sets the order of building the libraries.
+ #LIBS_TO_BUILD=aldor axllib debuglib algebra
+-LIBS_TO_BUILD=aldor axllib
++LIBS_TO_BUILD=aldor axllib algebra
+
+ # This is used to form the name of the tarball archive used for binary
diff --git a/dev-lang/aldor/metadata.xml b/dev-lang/aldor/metadata.xml
new file mode 100644
index 000000000..7b8af4e8c
--- /dev/null
+++ b/dev-lang/aldor/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>A.G.Grozin@inp.nsk.su</email>
+<name>Andrey Grozin</name>
+</maintainer>
+<longdescription lang="en">
+From a technical point of perspective, Aldor is a type-complete,
+strongly-typed, imperative programming language with a two-level
+object model of categories and domains (similar to the concept of
+interfaces and classes in Java). Types and functions are first class
+entities allowing them to be constructed and manipulated within
+Aldor programs just like any other value. Pervasive use of dependent
+types allows static checking of dynamic objects and provides
+object-oriented features such as parametric polymorphism.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-python/asciidata/ChangeLog b/dev-python/asciidata/ChangeLog
new file mode 100644
index 000000000..d04297436
--- /dev/null
+++ b/dev-python/asciidata/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for dev-python/asciidata
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*asciidata-1.0 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt>
+ +asciidata-1.0.ebuild, +metadata.xml
+ Initial import.
diff --git a/dev-python/asciidata/Manifest b/dev-python/asciidata/Manifest
new file mode 100644
index 000000000..79045f37f
--- /dev/null
+++ b/dev-python/asciidata/Manifest
@@ -0,0 +1,5 @@
+DIST asciidata-1.0.tar.gz 208115 RMD160 55f090dbd1b90837206f7e9ce68b86f2b13a0803 SHA1 108ba39cb919ddb199270db1f89580dfbb3f7f04 SHA256 20d820409ba0b7debbd93e8dd79a9566626513428fd18949ad789e032dccf05a
+DIST asciidata_1.0.tar.gz 104648 RMD160 2066ca255272459790a5dc16a61174f82020b138 SHA1 6425a4eb781eb051522f10aafe854369b104a4a7 SHA256 5a2dabe1e2135db4a04f7a9d8e7eaf952356da55a8498a261feb0a437e914dfc
+EBUILD asciidata-1.0.ebuild 605 RMD160 fba365f4948ce76a5e10ebc7a0e7465ccac0eff7 SHA1 1695190dfd0397dfba6511246d10391d052511e9 SHA256 a02e969225b8ce1e78e52458e0bef50d8d09128e821c72e6d491f120d5c612ae
+MISC ChangeLog 257 RMD160 ee69aa2ed9db02e9f388eb47ee3030237f4d3af6 SHA1 17f9a2304607c0c7e48687a34170f48ff1960a70 SHA256 0dbbc11cf469c0f1c4543f78782d4faf951aad8d4cbc8cfea237f139c00313d4
+MISC metadata.xml 450 RMD160 f1fd6a7506bf4680e443c4444e838c920a47fab8 SHA1 59d2acea5be821cfee9f363273ad9b7822a989b6 SHA256 b9d5f1a73e94560204c68661bb3b14507a68d3058d78cb65ee121e87f7462557
diff --git a/dev-python/asciidata/asciidata-1.0.ebuild b/dev-python/asciidata/asciidata-1.0.ebuild
new file mode 100644
index 000000000..e689797a6
--- /dev/null
+++ b/dev-python/asciidata/asciidata-1.0.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit distutils
+
+DESCRIPTION="Python module to handle ASCII tables"
+SRC_URI="http://www.stecf.org/software/PYTHONtools/astro${PN}/source/${P}.tar.gz
+ doc? ( http://www.stecf.org/software/PYTHONtools/astro${PN}/manual/${PN}_${PV}.tar.gz )"
+HOMEPAGE="http://www.stecf.org/software/astroasciidata/index.html"
+
+DEPEND="dev-python/numarray"
+IUSE="doc"
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+LICENSE="GPL-2"
+
+src_install() {
+ distutils_src_install
+ use doc && dohtml "${WORKDIR}"/asciidata/*
+}
diff --git a/dev-python/asciidata/metadata.xml b/dev-python/asciidata/metadata.xml
new file mode 100644
index 000000000..4f6d8e18c
--- /dev/null
+++ b/dev-python/asciidata/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ AsciiData is a Python module to handle ASCII tables. With this
+ module it is possible to:
+ * read ASCII tables;
+ * access its elements for reading and writing;
+ * save the ASCII table back to a file;
+ * delete/add rows and columns.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-python/visual/ChangeLog b/dev-python/visual/ChangeLog
new file mode 100644
index 000000000..08f2cec06
--- /dev/null
+++ b/dev-python/visual/ChangeLog
@@ -0,0 +1,73 @@
+# ChangeLog for dev-python/visual
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-python/visual/ChangeLog,v 1.16 2007/03/05 03:10:14 genone Exp $
+
+*visual-4.0_beta16 (18 Oct 2007)
+
+ 18 Oct 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +visual-4_beta16:
+ The current beta, fixes the bug #176431
+
+ 05 Mar 2007; Marius Mauch <genone@gentoo.org> visual-3.2.9.ebuild,
+ visual-4_beta0.ebuild:
+ Replacing einfo with elog
+
+ 24 Sep 2006; <blubb@gentoo.org> visual-3.2.9.ebuild:
+ marked ~amd64
+
+ 20 Jul 2006; Simon Stelling <blubb@gentoo.org> visual-3.2.9.ebuild,
+ visual-4_beta0.ebuild:
+ fixup multilib libdir paths
+
+ 16 Jul 2006; Tobias Scherbaum <dertobi123@gentoo.org> visual-3.2.9.ebuild:
+ ppc stable
+
+ 12 Jul 2006; Aron Griffis <agriffis@gentoo.org> visual-3.2.9.ebuild:
+ Mark 3.2.9 stable on ia64
+
+*visual-4_beta0 (24 Jun 2006)
+
+ 24 Jun 2006; Colin Kingsley <tercel@gentoo.org> visual-3.2.9.ebuild,
+ +visual-4_beta0.ebuild:
+ Add beta version under package.mask
+
+ 23 Apr 2006; <tercel@gentoo.org> -visual-3.2.5.ebuild,
+ -visual-3.2.7.ebuild, visual-3.2.9.ebuild:
+ move version 3.2.9 to stable for x86, and remove old versions.
+
+ 20 Apr 2006; Tobias Scherbaum <dertobi123@gentoo.org> visual-3.2.9.ebuild:
+ Added to ~ppc, bug #130564
+
+ 01 Apr 2006; Aron Griffis <agriffis@gentoo.org> visual-3.2.9.ebuild:
+ Mark 3.2.9 ~ia64
+
+ 02 Mar 2006; Marien Zwart <marienz@gentoo.org> metadata.xml:
+ Add to the python herd.
+
+*visual-3.2.9 (02 Mar 2006)
+
+ 02 Mar 2006; <tercel@gentoo.org> -visual-3.2.1.ebuild, visual-3.2.7.ebuild,
+ +visual-3.2.9.ebuild:
+ remove old stable version, stabilize newer version, add newest version to ~x86
+
+*visual-3.2.7 (13 Feb 2006)
+
+ 13 Feb 2006; <tercel@gentoo.org> visual-3.2.5.ebuild, +visual-3.2.7.ebuild:
+ Added version 3.2.7 to ~x86 and moved 3.2.5 to stable.
+
+*visual-3.2.5 (22 Dec 2005)
+
+ 22 Dec 2005; <tercel@gentoo.org> +visual-3.2.5.ebuild:
+ commit new version to ~x86
+
+ 11 Sep 2005; Jonathan Smith <smithj@gentoo.org> visual-3.2.1.ebuild:
+ fixed dependency... changed >=gtkglarea-1.2 to =1.2*
+
+ 13 Jul 2005; <tercel@gentoo.org> visual-3.2.1.ebuild:
+ 3.2.1 moved to stable on x86
+
+*visual-3.2.1 (01 Jun 2005)
+
+ 01 Jun 2005; <tercel@gentoo.org> +metadata.xml, +visual-3.2.1.ebuild:
+ Initial commit.
+
diff --git a/dev-python/visual/Manifest b/dev-python/visual/Manifest
new file mode 100644
index 000000000..f49e27ec3
--- /dev/null
+++ b/dev-python/visual/Manifest
@@ -0,0 +1,4 @@
+DIST visual-4.beta16.tar.bz2 603270 RMD160 8d8eb4ce4a4ccc70a5d445099e0ebc09e2024b0c SHA1 c6f8b9d5a8b7cb45a2ede7bebb284597fa92b3b8 SHA256 68590fafc9311a57e1c89b1f7d9574cc4a37ccbcf1c3502d8e99ad756d1e6d07
+EBUILD visual-4_beta16.ebuild 1913 RMD160 761cad44844adfcd929e6577509b004775038893 SHA1 e5c0a89cd55bad13bacd9c1bdadbfdb5ce3515f5 SHA256 bb25cdbb59b28cf3b20c9d10279caf2e7b361222c368abab9c3ea400a25d32ec
+MISC ChangeLog 2322 RMD160 31e46e141e73ec27176ca1e9e81a82941d7cb025 SHA1 413847895ac7b9899c32e1f7fadcc59d068a5089 SHA256 85953f1e6915610697b70fa50036ae2716847e7794fee6e7d15ca6e1d223ec7b
+MISC metadata.xml 254 RMD160 aeedd5899011a058906b650ddb6b35d16f54c026 SHA1 47dd380154630bc0f52348da83c300ea24dc713c SHA256 87134ddff75392b185570f1dfbfd76d7bcfccfefef6d7c5a548a876a701fc792
diff --git a/dev-python/visual/metadata.xml b/dev-python/visual/metadata.xml
new file mode 100644
index 000000000..e54446668
--- /dev/null
+++ b/dev-python/visual/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>python</herd>
+ <maintainer>
+ <email>tercel@gentoo.org</email>
+ <name>Colin Kingsley</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/visual/visual-4_beta16.ebuild b/dev-python/visual/visual-4_beta16.ebuild
new file mode 100644
index 000000000..9b67bb27d
--- /dev/null
+++ b/dev-python/visual/visual-4_beta16.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-python/visual/visual-4_beta0.ebuild,v 1.3 2007/03/05 03:10:14 genone Exp $
+
+inherit distutils versionator multilib
+
+MY_P=$(replace_version_separator _ . ${P})
+
+S="${WORKDIR}/${MY_P}"
+
+DESCRIPTION="An easy to use Real-time 3D graphics library for Python."
+SRC_URI="http://www.vpython.org/download/${MY_P}.tar.bz2"
+HOMEPAGE="http://www.vpython.org/"
+
+IUSE="doc examples numeric numarray"
+SLOT="0"
+KEYWORDS="~x86"
+LICENSE="visual"
+
+DEPEND=">=dev-lang/python-2.2
+ >=dev-libs/boost-1.31
+ virtual/opengl
+ =dev-cpp/gtkglextmm-1.2*
+ dev-cpp/libglademm
+ numeric? ( dev-python/numeric )
+ numarray? ( >=dev-python/numarray-1.0 )
+ !numeric? ( !numarray? ( dev-python/numeric ) )"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ local myconf="--without-numarray --without-numeric"
+
+ echo
+ if use numeric; then
+ elog "Building with Numeric support"
+ myconf=${myconf/--without-numeric}
+ fi
+ if use numarray; then
+ elog "Building with Numarray support"
+ myconf=${myconf/--without-numarray}
+ fi
+ if ! use numeric && ! use numarray; then
+ elog "Support for Numeric or Numarray was not specified."
+ elog "Building with Numeric support"
+ myconf=${myconf/--without-numeric}
+ fi
+ echo
+
+ econf \
+ --with-html-dir=/usr/share/doc/${PF}/html \
+ --with-example-dir=/usr/share/doc/${PF}/examples \
+ $(use_enable doc docs) \
+ $(use_enable examples) \
+ ${myconf} \
+ || die "econf failed"
+
+ sed -i s/boost_thread/boost_thread-mt/ src/Makefile
+
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+
+ python_version
+
+ mv "${D}"/usr/$(get_libdir)/python${PYVER}/site-packages/cvisualmodule* \
+ "${D}"/usr/$(get_libdir)/python${PYVER}/site-packages/visual
+
+ #the vpython script does not work, and is unnecessary
+ rm "${D}"/usr/bin/vpython
+}
diff --git a/dev-tcltk/tkimg/ChangeLog b/dev-tcltk/tkimg/ChangeLog
new file mode 100644
index 000000000..ff524eaed
--- /dev/null
+++ b/dev-tcltk/tkimg/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for dev-tcltk/tkimg
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org> tkimg-1.3.ebuild:
+ cleaning
+
+*tkimg-1.3 (14 Sep 2006)
+
+ 14 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ +tkimg-1.3.ebuild, +metadata.xml,
+ +files/tkimg-1.3-m4.patch
+ +files/tkimg-1.3-makedeps.patch
+ +files/tkimg-1.3-syslibs.patch
+ +files/tkimg-1.3-warnings.patch
+ Initial import.
+
diff --git a/dev-tcltk/tkimg/Manifest b/dev-tcltk/tkimg/Manifest
new file mode 100644
index 000000000..7c69d3f5a
--- /dev/null
+++ b/dev-tcltk/tkimg/Manifest
@@ -0,0 +1,8 @@
+AUX tkimg-1.3-m4.patch 9543 RMD160 e3a156f8a87a6f6f7967b81e73a0bb98a78176c3 SHA1 d66f86b79101765e2f9a7fd072011638a0ddbad6 SHA256 409b9877daf172113052a689a7eeb9a9226965356a8b9ddfa0947bca0d8f08d9
+AUX tkimg-1.3-makedeps.patch 3022 RMD160 f04e0912380e2669f0221e6eae1372b886dd3c9b SHA1 229b69285bb035e4bc0dc8b4d9d059cf139668ff SHA256 5b359d562d793e65791ae6dceb7eeae0d740b471b8362bc02515c9fa0ad19bd6
+AUX tkimg-1.3-syslibs.patch 12672 RMD160 c5f5f9a8275d92afaeb40f1a7584a0102d12ee08 SHA1 fde468d011e576854354a805ff5603df53a4042e SHA256 fcac1bf27bfb7e1adb8bbdb503c7449533c29de91bf5cfe1333dbea7017936a0
+AUX tkimg-1.3-warnings.patch 833 RMD160 80f45f8d830a3b69dfd983a098ec000d48bbedf9 SHA1 fdb6f263416d0cefccbc5c2c5f3067c1753efd52 SHA256 51b907379959ccf6d474300ba801c722b0d316e88bf5b1c033049b554b3700c1
+DIST tkimg1.3.tar.bz2 2924740 RMD160 fb0992c72faeb80fc6aaa2ccb1f632087235ea9d SHA1 b2d97cf80f9cd457a194b0d2c4bd549a66783895 SHA256 3daebe7c4a3d15e175a0203ada94adc2b78403d164d9fe9797e274e6256fcf33
+EBUILD tkimg-1.3.ebuild 1055 RMD160 46c66f94e173de2f71147cbecda793e4936b1aa9 SHA1 c2de369e9eb9951f4f713ccea0cbf99aacb82fc0 SHA256 8a2cfdc1d15c14cf091bac3bbca69164d090d19d3e58ee13f04267a6b0e8fd54
+MISC ChangeLog 465 RMD160 36ba1d94f48b4c9681cdf35b8556bf3d734973e6 SHA1 d530c9f147987e157dce2e37dc88702940db456e SHA256 0cc94d33068e2ec2d3e1b860d4f9a027f9764f6566feac516caa6084dd1a0dd4
+MISC metadata.xml 252 RMD160 3ae378dbda1cda6f29fc8d12d7ed3043e1df5cbc SHA1 6283b36b1f69d450f2f77dd456acb17c83485b96 SHA256 57ba6f7e8d62b8c319f2e4e55658b3d134ff5223443e4383316a23d150b9232a
diff --git a/dev-tcltk/tkimg/files/tkimg-1.3-m4.patch b/dev-tcltk/tkimg/files/tkimg-1.3-m4.patch
new file mode 100644
index 000000000..d1814b649
--- /dev/null
+++ b/dev-tcltk/tkimg/files/tkimg-1.3-m4.patch
@@ -0,0 +1,311 @@
+--- Makefile.in
++++ Makefile.in
+@@ -117,12 +117,14 @@
+ here=`pwd` ; \
+ cd $$sub ; \
+ $(MAKE) install \
++ DESTDIR="" INSTALL_ROOT="" \
++ libdir=$$here/Img/exec_prefix/lib \
+ exec_prefix=$$here/Img/exec_prefix \
+ prefix=$$here/Img/prefix \
+ pkglibdir=$$here/Img/exec_prefix/lib/Img \
+ ; \
+ cd $$here ; \
+- cat Img/exec_prefix/lib/Img/pkgIndex.tcl >> pkgIndex.tcl ; \
++ cat Img/exec_prefix/lib/Img/pkgIndex.tcl >> pkgIndex.tcl || :; \
+ done
+ mv pkgIndex.tcl Img/exec_prefix/lib/Img/pkgIndex.tcl
+
+--- base/tclconfig/tcl.m4
++++ base/tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- base/tkimg.h
++++ base/tkimg.h
+@@ -22,6 +22,7 @@
+ #define __TKIMG_H__
+
+ #include <stdio.h> /* stdout, and other definitions */
++#include <string.h>
+ #include "tk.h"
+
+ /*
+--- libjpeg/tcl/configure
++++ libjpeg/tcl/configure
+@@ -5319,14 +5319,14 @@
+
+ case "$srcdir" in
+ .) # No --srcdir option. We are building in place.
+- jpegdir=$srcdir/.. ;;
++ jpegdir=`pwd`/.. ;;
+ /*) # Absolute path.
+ jpegdir=$srcdir/.. ;;
+ *) # Relative path.
+ jpegdir=../$ac_dots$srcdir/.. ;;
+ esac
+
+-mkdir libjpeg
++mkdir -p libjpeg
+ cd libjpeg
+ env CC="$JPEG_CC" CFLAGS="$JPEG_CFLAGS" $jpegdir/configure
+ cd ..
+--- libjpeg/tcl/tclconfig/tcl.m4
++++ libjpeg/tcl/tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- libpng/tcl/tclconfig/tcl.m4
++++ libpng/tcl/tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- libtiff/tcl/tclconfig/tcl.m4
++++ libtiff/tcl/tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- libz/tcl/tclconfig/tcl.m4
++++ libz/tcl/tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- tclconfig/tcl.m4
++++ tclconfig/tcl.m4
+@@ -759,7 +759,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
+@@ -1143,7 +1143,7 @@
+ # is kind of overkill but it works.
+ # Disable inlining only when one of the
+ # files in compat/*.c is being linked in.
+- if test x"${LIBOBJS}" != x ; then
++ if test x"${LIB@&t@OBJS}" != x ; then
+ EXTRA_CFLAGS="${EXTRA_CFLAGS} -fno-inline"
+ fi
+
+@@ -2026,7 +2026,7 @@
+ # results, and the version is kept in special file).
+
+ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
++ system=MP-RAS-`awk '{print $3}' /etc/.relid`
+ fi
+ if test "`uname -s`" = "AIX" ; then
+ system=AIX-`uname -v`.`uname -r`
diff --git a/dev-tcltk/tkimg/files/tkimg-1.3-makedeps.patch b/dev-tcltk/tkimg/files/tkimg-1.3-makedeps.patch
new file mode 100644
index 000000000..ef6696676
--- /dev/null
+++ b/dev-tcltk/tkimg/files/tkimg-1.3-makedeps.patch
@@ -0,0 +1,176 @@
+--- bmp/Makefile.in
++++ bmp/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- gif/Makefile.in
++++ gif/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- ico/Makefile.in
++++ ico/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- jpeg/Makefile.in
++++ jpeg/Makefile.in
+@@ -322,7 +322,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- pcx/Makefile.in
++++ pcx/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- pixmap/Makefile.in
++++ pixmap/Makefile.in
+@@ -324,7 +324,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- png/Makefile.in
++++ png/Makefile.in
+@@ -322,7 +322,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- ppm/Makefile.in
++++ ppm/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- ps/Makefile.in
++++ ps/Makefile.in
+@@ -320,7 +320,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- sgi/Makefile.in
++++ sgi/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- sun/Makefile.in
++++ sun/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- tga/Makefile.in
++++ tga/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- tiff/Makefile.in
++++ tiff/Makefile.in
+@@ -322,7 +322,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- window/Makefile.in
++++ window/Makefile.in
+@@ -323,7 +323,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- xbm/Makefile.in
++++ xbm/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
+--- xpm/Makefile.in
++++ xpm/Makefile.in
+@@ -318,7 +318,7 @@
+
+ VPATH = $(srcdir)
+
+-.c.$(OBJEXT):
++.c.$(OBJEXT): init.c
+ $(COMPILE) -c `@CYGPATH@ $<` -o $@
+
+ init.c: $(srcdir)/../init.c
diff --git a/dev-tcltk/tkimg/files/tkimg-1.3-syslibs.patch b/dev-tcltk/tkimg/files/tkimg-1.3-syslibs.patch
new file mode 100644
index 000000000..9ff0b5774
--- /dev/null
+++ b/dev-tcltk/tkimg/files/tkimg-1.3-syslibs.patch
@@ -0,0 +1,441 @@
+--- configure.in
++++ configure.in
+@@ -43,24 +43,20 @@
+ CC=`echo $CC | sed -e 's/ .*$//'`
+
+ TEA_CONFIG_COLLECT
+-TEA_CONFIG_SUBDIR(libz/tcl, [])
+-TEA_CONFIG_SUBDIR(libpng/tcl, [--with-zlibtcl=`pwd`/libz/tcl])
+-TEA_CONFIG_SUBDIR(libtiff/tcl,[])
+-TEA_CONFIG_SUBDIR(libjpeg/tcl,[])
+ TEA_CONFIG_SUBDIR(base, [])
+ TEA_CONFIG_SUBDIR(bmp, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(gif, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(ico, [--with-tkimg=`pwd`/base])
+-TEA_CONFIG_SUBDIR(jpeg, [--with-tkimg=`pwd`/base --with-jpegtcl=`pwd`/libjpeg/tcl])
++TEA_CONFIG_SUBDIR(jpeg, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(pcx, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(pixmap, [--with-tkimg=`pwd`/base])
+-TEA_CONFIG_SUBDIR(png, [--with-tkimg=`pwd`/base --with-pngtcl=`pwd`/libpng/tcl --with-zlibtcl=`pwd`/libz/tcl])
++TEA_CONFIG_SUBDIR(png, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(ppm, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(ps, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(sgi, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(sun, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(tga, [--with-tkimg=`pwd`/base])
+-TEA_CONFIG_SUBDIR(tiff, [--with-tkimg=`pwd`/base --with-tifftcl=`pwd`/libtiff/tcl --with-zlibtcl=`pwd`/libz/tcl --with-jpegtcl=`pwd`/libjpeg/tcl])
++TEA_CONFIG_SUBDIR(tiff, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(window, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(xbm, [--with-tkimg=`pwd`/base])
+ TEA_CONFIG_SUBDIR(xpm, [--with-tkimg=`pwd`/base])
+--- jpeg/Makefile.in
++++ jpeg/Makefile.in
+@@ -51,10 +51,6 @@
+ ## tkimgjpegstub_OBJECTS = tkimgjpegStubLib.$(OBJEXT)
+ ## tkimgjpegstub_LIB_FILE= @tkimgjpegstub_LIB_FILE@
+
+-jpegtcl_SRC_PATH = @jpegtcl_SRC_PATH@
+-jpegtcl_BUILD_PATH = @jpegtcl_BUILD_PATH@
+-jpegtcl_VERSION = @jpegtcl_VERSION@
+-
+ tkimg_SRC_PATH = @tkimg_SRC_PATH@
+ tkimg_BUILD_PATH = @tkimg_BUILD_PATH@
+ tkimg_VERSION = @tkimg_VERSION@
+@@ -189,8 +185,6 @@
+
+ INCLUDES = \
+ -I$(tkimg_SRC_PATH) \
+- -I$(jpegtcl_SRC_PATH) \
+- -I$(jpegtcl_BUILD_PATH)/libjpeg \
+ -I. -I$(srcdir) \
+ @TCL_INCLUDES@ \
+ @TK_INCLUDES@ \
+@@ -202,8 +196,7 @@
+
+ CONFIG_CLEAN_FILES = Makefile pkgIndex.tcl
+
+-CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\" \
+- -DJPEGTCL_VERSION=\"$(jpegtcl_VERSION)\" \
++CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\"
+
+ LIBS = @LIBS@
+ AR = ar
+--- jpeg/configure.in
++++ jpeg/configure.in
+@@ -95,11 +95,6 @@
+ TEA_PATH_CONFIG(tkimg)
+ TEA_LOAD_CONFIG(tkimg)
+
+-TEA_PATH_CONFIG(jpegtcl)
+-TEA_LOAD_CONFIG(jpegtcl)
+-AC_SUBST(jpegtcl_VERSION)
+-
+-IMG_SRCPATH(jpegtcl)
+ IMG_SRCPATH(tkimg)
+
+ #--------------------------------------------------------------------
+@@ -186,7 +181,6 @@
+ AC_DEFINE(USE_TCL_STUBS)
+ AC_DEFINE(USE_TK_STUBS)
+ AC_DEFINE(USE_TKIMG_STUBS)
+-AC_DEFINE(USE_JPEGTCL_STUBS)
+
+ #--------------------------------------------------------------------
+ # This macro generates a line to use when building a library. It
+@@ -203,13 +197,11 @@
+
+ if test "${TEA_PLATFORM}" = "windows" -a "$GCC" != "yes" ; then
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${tkimg_STUB_LIB_PATH}`\""
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${jpegtcl_STUB_LIB_PATH}`\""
+ else
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${tkimg_STUB_LIB_SPEC}"
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${jpegtcl_STUB_LIB_SPEC}"
+ fi
+
+-SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \${TK_LIBS}"
++SHLIB_LD_LIBS="${SHLIB_LD_LIBS} -ljpeg \${TK_LIBS}"
+
+ #--------------------------------------------------------------------
+ # Find tclsh so that we can run pkg_mkIndex to generate the pkgIndex.tcl
+--- jpeg/jpeg.c
++++ jpeg/jpeg.c
+@@ -53,9 +53,10 @@
+ */
+
+ #include <stdio.h>
+-
+-#include <tcl.h>
+-#include <jpegtcl.h>
++#include <sys/types.h>
++#include <jpeglib.h>
++#include <jerror.h>
++#include <tk.h>
+
+ static int SetupJPegLibrary _ANSI_ARGS_ ((Tcl_Interp *interp));
+
+@@ -145,10 +146,6 @@
+ struct my_error_mgr jerror; /* for controlling libjpeg error handling */
+ int i;
+
+- if (Jpegtcl_InitStubs(interp, "1.0", 0) == NULL) {
+- return TCL_ERROR;
+- }
+-
+ /* The followin code tries to determine if the JPEG library is
+ valid at all. The library might be configured differently,
+ which will produce core dumps. Also it might be that
+--- png/Makefile.in
++++ png/Makefile.in
+@@ -51,14 +51,6 @@
+ ## tkimgpngstub_OBJECTS = tkimgpngStubLib.$(OBJEXT)
+ ## tkimgpngstub_LIB_FILE= @tkimgpngstub_LIB_FILE@
+
+-pngtcl_SRC_PATH = @pngtcl_SRC_PATH@
+-pngtcl_BUILD_PATH = @pngtcl_BUILD_PATH@
+-pngtcl_VERSION = @pngtcl_VERSION@
+-
+-zlibtcl_SRC_PATH = @zlibtcl_SRC_PATH@
+-zlibtcl_BUILD_PATH = @zlibtcl_BUILD_PATH@
+-zlibtcl_VERSION = @zlibtcl_VERSION@
+-
+ tkimg_SRC_PATH = @tkimg_SRC_PATH@
+ tkimg_BUILD_PATH = @tkimg_BUILD_PATH@
+ tkimg_VERSION = @tkimg_VERSION@
+@@ -193,10 +185,6 @@
+
+ INCLUDES = \
+ -I$(tkimg_SRC_PATH) \
+- -I$(pngtcl_SRC_PATH) \
+- -I$(pngtcl_BUILD_PATH) \
+- -I$(zlibtcl_SRC_PATH) \
+- -I$(zlibtcl_BUILD_PATH) \
+ -I. -I$(srcdir) \
+ @TCL_INCLUDES@ \
+ @TK_INCLUDES@ \
+@@ -208,9 +196,7 @@
+
+ CONFIG_CLEAN_FILES = Makefile pkgIndex.tcl
+
+-CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\" \
+- -DPNGTCL_VERSION=\"$(pngtcl_VERSION)\" \
+- -DPNGTCL_VERSION=\"$(zlibtcl_VERSION)\"
++CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\"
+
+ LIBS = @LIBS@
+ AR = ar
+--- png/configure.in
++++ png/configure.in
+@@ -95,17 +95,7 @@
+ TEA_PATH_CONFIG(tkimg)
+ TEA_LOAD_CONFIG(tkimg)
+
+-TEA_PATH_CONFIG(pngtcl)
+-TEA_LOAD_CONFIG(pngtcl)
+-AC_SUBST(pngtcl_VERSION)
+-
+-TEA_PATH_CONFIG(zlibtcl)
+-TEA_LOAD_CONFIG(zlibtcl)
+-AC_SUBST(zlibtcl_VERSION)
+-
+ IMG_SRCPATH(tkimg)
+-IMG_SRCPATH(pngtcl)
+-IMG_SRCPATH(zlibtcl)
+
+ #--------------------------------------------------------------------
+ # __CHANGE__
+@@ -191,8 +181,6 @@
+ AC_DEFINE(USE_TCL_STUBS)
+ AC_DEFINE(USE_TK_STUBS)
+ AC_DEFINE(USE_TKIMG_STUBS)
+-AC_DEFINE(USE_PNGTCL_STUBS)
+-AC_DEFINE(USE_ZLIBTCL_STUBS)
+
+ #--------------------------------------------------------------------
+ # This macro generates a line to use when building a library. It
+@@ -209,13 +197,11 @@
+
+ if test "${TEA_PLATFORM}" = "windows" -a "$GCC" != "yes" ; then
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${tkimg_STUB_LIB_PATH}`\""
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${pngtcl_STUB_LIB_PATH}`\""
+ else
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${tkimg_STUB_LIB_SPEC}"
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${pngtcl_STUB_LIB_SPEC}"
+ fi
+
+-SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \${TK_LIBS}"
++SHLIB_LD_LIBS="${SHLIB_LD_LIBS} -lpng \${TK_LIBS}"
+
+ #--------------------------------------------------------------------
+ # Find tclsh so that we can run pkg_mkIndex to generate the pkgIndex.tcl
+--- png/png.c
++++ png/png.c
+@@ -21,7 +21,7 @@
+ */
+
+ #include <tcl.h>
+-#include <pngtcl.h>
++#include <png.h>
+ #include <string.h>
+ #include <stdlib.h>
+
+@@ -108,9 +108,6 @@
+ SetupPngLibrary (interp)
+ Tcl_Interp *interp;
+ {
+- if (Pngtcl_InitStubs(interp, PNGTCL_VERSION, 0) == NULL) {
+- return TCL_ERROR;
+- }
+ return TCL_OK;
+ }
+
+--- tclconfig/tcl.m4
++++ tclconfig/tcl.m4
+@@ -912,7 +912,7 @@
+
+ # AIX v<=4.1 has some different flags than 4.2+
+ if test "$system" = "AIX-4.1" -o "`uname -v`" -lt "4" ; then
+- LIBOBJS="$LIBOBJS tclLoadAix.o"
++ AC_LIBOBJ([tclLoadAix])
+ DL_LIBS="-lld"
+ fi
+
+@@ -2178,7 +2178,7 @@
+ AC_MSG_RESULT([ok])
+ else
+ AC_MSG_RESULT([buggy])
+- LIBOBJS="$LIBOBJS fixstrtod.o"
++ AC_LIBOBJ([fixstrtod])
+ AC_DEFINE(strtod, fixstrtod)
+ fi
+ fi
+--- tiff/Makefile.in
++++ tiff/Makefile.in
+@@ -28,9 +28,6 @@
+
+ tkimgtiff_SOURCES = \
+ tiff.c \
+- tiffZip.c \
+- tiffJpeg.c \
+- tiffPixar.c \
+ @EXTRA_SOURCES@
+
+ WIN_SOURCES =
+@@ -54,18 +51,6 @@
+ ## tkimgtiffstub_OBJECTS = tkimgtiffStubLib.$(OBJEXT)
+ ## tkimgtiffstub_LIB_FILE= @tkimgtiffstub_LIB_FILE@
+
+-tifftcl_SRC_PATH = @tifftcl_SRC_PATH@
+-tifftcl_BUILD_PATH = @tifftcl_BUILD_PATH@
+-tifftcl_VERSION = @tifftcl_VERSION@
+-
+-jpegtcl_SRC_PATH = @jpegtcl_SRC_PATH@
+-jpegtcl_BUILD_PATH = @jpegtcl_BUILD_PATH@
+-jpegtcl_VERSION = @jpegtcl_VERSION@
+-
+-zlibtcl_SRC_PATH = @zlibtcl_SRC_PATH@
+-zlibtcl_BUILD_PATH = @zlibtcl_BUILD_PATH@
+-zlibtcl_VERSION = @zlibtcl_VERSION@
+-
+ tkimg_SRC_PATH = @tkimg_SRC_PATH@
+ tkimg_BUILD_PATH = @tkimg_BUILD_PATH@
+ tkimg_VERSION = @tkimg_VERSION@
+@@ -200,12 +185,6 @@
+
+ INCLUDES = \
+ -I$(tkimg_SRC_PATH) \
+- -I$(tifftcl_SRC_PATH) \
+- -I$(tifftcl_BUILD_PATH)/libtiff \
+- -I$(jpegtcl_SRC_PATH) \
+- -I$(jpegtcl_BUILD_PATH)/libjpeg \
+- -I$(zlibtcl_SRC_PATH) \
+- -I$(zlibtcl_BUILD_PATH) \
+ -I. -I$(srcdir) \
+ @TCL_INCLUDES@ \
+ @TK_INCLUDES@ \
+@@ -217,10 +196,7 @@
+
+ CONFIG_CLEAN_FILES = Makefile pkgIndex.tcl
+
+-CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\" \
+- -DTIFFTCL_VERSION=\"$(tifftcl_VERSION)\" \
+- -DJPEGTCL_VERSION=\"$(jpegtcl_VERSION)\" \
+- -DZLIBTCL_VERSION=\"$(zlibtcl_VERSION)\"
++CPPFLAGS = @CPPFLAGS@ -DPACKAGE_NAME=\"$(DPACKAGE)\"
+
+ LIBS = @LIBS@
+ AR = ar
+--- tiff/configure.in
++++ tiff/configure.in
+@@ -95,22 +95,7 @@
+ TEA_PATH_CONFIG(tkimg)
+ TEA_LOAD_CONFIG(tkimg)
+
+-TEA_PATH_CONFIG(tifftcl)
+-TEA_LOAD_CONFIG(tifftcl)
+-AC_SUBST(tifftcl_VERSION)
+-
+-TEA_PATH_CONFIG(jpegtcl)
+-TEA_LOAD_CONFIG(jpegtcl)
+-AC_SUBST(jpegtcl_VERSION)
+-
+-TEA_PATH_CONFIG(zlibtcl)
+-TEA_LOAD_CONFIG(zlibtcl)
+-AC_SUBST(zlibtcl_VERSION)
+-
+ IMG_SRCPATH(tkimg)
+-IMG_SRCPATH(tifftcl)
+-IMG_SRCPATH(jpegtcl)
+-IMG_SRCPATH(zlibtcl)
+
+ #--------------------------------------------------------------------
+ # __CHANGE__
+@@ -196,9 +181,6 @@
+ AC_DEFINE(USE_TCL_STUBS)
+ AC_DEFINE(USE_TK_STUBS)
+ AC_DEFINE(USE_TKIMG_STUBS)
+-AC_DEFINE(USE_TIFFTCL_STUBS)
+-AC_DEFINE(USE_JPEGTCL_STUBS)
+-AC_DEFINE(USE_ZLIBTCL_STUBS)
+
+ #--------------------------------------------------------------------
+ # This macro generates a line to use when building a library. It
+@@ -215,17 +197,11 @@
+
+ if test "${TEA_PLATFORM}" = "windows" -a "$GCC" != "yes" ; then
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${tkimg_STUB_LIB_PATH}`\""
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${tifftcl_STUB_LIB_PATH}`\""
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${jpegtcl_STUB_LIB_PATH}`\""
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \"`${CYGPATH} ${zlibtcl_STUB_LIB_PATH}`\""
+ else
+ SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${tkimg_STUB_LIB_SPEC}"
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${tifftcl_STUB_LIB_SPEC}"
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${jpegtcl_STUB_LIB_SPEC}"
+- SHLIB_LD_LIBS="${SHLIB_LD_LIBS} ${zlibtcl_STUB_LIB_SPEC}"
+ fi
+
+-SHLIB_LD_LIBS="${SHLIB_LD_LIBS} \${TK_LIBS}"
++SHLIB_LD_LIBS="${SHLIB_LD_LIBS} -ltiff \${TK_LIBS}"
+
+ #--------------------------------------------------------------------
+ # Find tclsh so that we can run pkg_mkIndex to generate the pkgIndex.tcl
+--- tiff/tiff.c
++++ tiff/tiff.c
+@@ -14,10 +14,7 @@
+ * Generic initialization code, parameterized via CPACKAGE and PACKAGE.
+ */
+
+-#include <tcl.h>
+-#include <tifftcl.h>
+-#include <jpegtcl.h>
+-#include <zlibtcl.h>
++#include <tk.h>
+
+ static int SetupTiffLibrary _ANSI_ARGS_ ((Tcl_Interp *interp));
+
+@@ -26,6 +23,8 @@
+
+ #include "init.c"
+
++#include <tiff.h>
++#include <tiffio.h>
+ #include <tiffInt.h>
+
+
+@@ -81,10 +80,6 @@
+ {
+ static int initialized = 0;
+
+- if (Tifftcl_InitStubs(interp, TIFFTCL_VERSION, 0) == NULL) {
+- return TCL_ERROR;
+- }
+-
+ if (errorMessage) {
+ ckfree(errorMessage);
+ errorMessage = NULL;
+@@ -96,35 +91,8 @@
+ TIFFSetWarningHandler(_TIFFwarn);
+ }
+
+- /*
+- * Initialize jpeg and zlib too, for use by the CODEC's we register
+- * with the base TIFF library in this package.
+- */
+-
+- if (Jpegtcl_InitStubs(interp, "1.0", 0) == NULL) {
+- return TCL_ERROR;
+- }
+-
+ if (!initialized) {
+ initialized = 1;
+- if (
+- TIFFRegisterCODEC && TIFFError && TIFFPredictorInit &&
+- TIFFMergeFieldInfo && TIFFFlushData1 && _TIFFNoPostDecode &&
+- TIFFTileRowSize && TIFFScanlineSize && _TIFFsetByteArray &&
+- TIFFVSetField && TIFFSwabArrayOfShort
+- ) {
+-
+- if (Zlibtcl_InitStubs(interp, "1.0", 0) == NULL) {
+- return TCL_ERROR;
+- }
+- TIFFRegisterCODEC (COMPRESSION_DEFLATE, "Deflate", TkimgTIFFInitZip);
+-
+- if (Jpegtcl_InitStubs(interp, "1.0", 0) == NULL) {
+- return TCL_ERROR;
+- }
+- TIFFRegisterCODEC (COMPRESSION_JPEG, "JPEG", TkimgTIFFInitJpeg);
+- TIFFRegisterCODEC (COMPRESSION_PIXARLOG, "PixarLog", TkimgTIFFInitPixar);
+- }
+ }
+ return TCL_OK;
+ }
+--- tiff/tiffInt.h
++++ tiff/tiffInt.h
+@@ -2,7 +2,7 @@
+ * tiffInit.h --
+ */
+
+-#include <tifftcl.h>
++#include <tiff.h>
+
+ /*
+ * Declarations shared between the .c files of the TIFF format handler.
diff --git a/dev-tcltk/tkimg/files/tkimg-1.3-warnings.patch b/dev-tcltk/tkimg/files/tkimg-1.3-warnings.patch
new file mode 100644
index 000000000..5151b84f2
--- /dev/null
+++ b/dev-tcltk/tkimg/files/tkimg-1.3-warnings.patch
@@ -0,0 +1,35 @@
+--- bmp/bmp.c
++++ bmp/bmp.c
+@@ -446,9 +446,7 @@
+ }
+ if ((rleBuf[0]==0) && (rleBuf[1]==2)) {
+ /* Deltarecord */
+- /* printf ("Deltarecord\n"); fflush (stdout); */
+- x += rleBuf[2];
+- y += rleBuf[3];
++ Tcl_AppendResult(interp, "Delta records not supported.", (char *)NULL);
+ }
+ }
+ }
+--- ps/ps.c
++++ ps/ps.c
+@@ -171,7 +171,7 @@
+ (tkimg_Read(handle, (char *) buf, 40) == 40))) {
+ int w, h, zoomx, zoomy;
+ char *p = buf;
+- buf[41] = 0;
++ buf[40] = 0;
+ w = - (int) strtoul(p, &p, 0);
+ h = - (int) strtoul(p, &p, 0);
+ w += strtoul(p, &p, 0);
+--- tiff/tiff.c
++++ tiff/tiff.c
+@@ -561,7 +561,7 @@
+ int srcX, srcY;
+ {
+ myblock bl;
+- unsigned char *pixelPtr = block.pixelPtr;
++ unsigned char *pixelPtr;
+ uint32 w, h;
+ size_t npixels;
+ uint32 *raster;
diff --git a/dev-tcltk/tkimg/metadata.xml b/dev-tcltk/tkimg/metadata.xml
new file mode 100644
index 000000000..384a7ca04
--- /dev/null
+++ b/dev-tcltk/tkimg/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>tcltk</herd>
+<longdescription>
+The "Img" package adds a lot of image formats to Tcl/Tk.
+</longdescription>
+</pkgmetadata>
diff --git a/dev-tcltk/tkimg/tkimg-1.3.ebuild b/dev-tcltk/tkimg/tkimg-1.3.ebuild
new file mode 100644
index 000000000..974fa218a
--- /dev/null
+++ b/dev-tcltk/tkimg/tkimg-1.3.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils autotools
+
+MY_P="${PN}${PV}"
+DESCRIPTION="Adds a lot of image formats to Tcl/Tk"
+HOMEPAGE="http://sourceforge.net/projects/tkimg/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
+
+IUSE=""
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-lang/tk
+ media-libs/libpng
+ media-libs/tiff"
+
+S=${WORKDIR}/${MY_P}
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-m4.patch
+ epatch "${FILESDIR}"/${P}-syslibs.patch
+ epatch "${FILESDIR}"/${P}-makedeps.patch
+ epatch "${FILESDIR}"/${P}-warnings.patch
+ rm -f $(find . -name configure)
+ for i in $(find -type d); do
+ cd "${S}"/${i}
+ [ -f configure.in ] && eautoreconf
+ done
+}
+
+src_install() {
+ emake \
+ DESTDIR="${D}" \
+ INSTALL_ROOT="${D}" \
+ install || die "emake install failed"
+ dodoc ChangeLog README Reorganization.Notes.txt changes ANNOUNCE
+ insinto /usr/share/doc/${PF}/demo
+ doins -r demo/*
+ doman doc/man/*
+ use doc && dohtml doc/html
+}
diff --git a/eclass/mpi.eclass b/eclass/mpi.eclass
new file mode 100644
index 000000000..deac1d848
--- /dev/null
+++ b/eclass/mpi.eclass
@@ -0,0 +1,412 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# Description: This eclass is used to allow for the separation of mpi
+# implementations and dependant programs/libraries in
+# /usr/lib/mpi/<implementation>.
+#
+# Author(s): Justin Bronder <jsbronder@gentoo.org>
+#
+# Basic idea is directly stolen from crossdev and hence really relies on using
+# sys-cluster/empi. EmergeMPI basically creates new categories, pulls in a
+# single MPI providing ebuild that uses this eclass and builds. This eclass
+# handles pushing the entire install to a save place, /usr/lib/mpi/<name>.
+# Packages that depend on MPI can also use this eclass to get installed to
+# the same place using the correct MPI implementation.
+
+# Currently only autotools-enabled packages are handled with any sort of
+# elegance, and dealing with the standard Makefile-style builds that
+# are typical in hpc probably can't be made much easier.
+
+# NOTE: If using this eclass to build an implementation, you need to define
+# MPI_ESELECT_FILE which is the path relative to FILESDIR where the eselect
+# definition file can be found.
+
+
+# FUNCTIONS, at least those that are worth caring about!
+
+# mpi_src_compile: For each implementation, set $S correctly and then run
+# through do_config and do_make. Finally restore $S
+
+# mpi_src_install: For each implementation, set $S correctly, run
+# do_make_install and restore $S.
+
+# mpi_pkg_deplist: Prints deps for mpi enabled packages. Basically if using
+# empi, then we dep on empi-enabled implementations,
+# otherwise, the dep is just on virtual/mpi
+
+# mpi_imp_deplist: Prints deps for mpi implementations. As empi guarantees
+# blockers cannot be installed at the same root, this deps
+# on eselect-mpi for empi builds. Otherwise, prints a list
+# of blockers (all other mpi implementations).
+
+# mpi_built_with: Get the ${PN} of the implementation that was used to get
+# mpicc etc.
+
+# get_mpi_dir: Given an implementation, returns the base directory to
+# that programs should install to. I.E. --prefix for
+# autoconf.
+
+# is_empi_build: Are we building with empi? [[ ${CATEGORY} == mpi-* ]] as
+# empi forces this just so we can do that.
+
+# FUNCTIONS, directly used by the above interesting ones.
+
+# mpi_set_env <imp>: For lack of a better name, just exports the following based
+# on the desired implementation: CC, CXX, F77, FC, PATH
+# Set $mpi_env to "mpi_none" to ensure that this function
+# is not called.
+
+# mpi_restore_env: Undo the above.
+
+# For the following functions and those that call them, I've used indirect
+# referencing to allow for a clean way to have both defaults and to allow
+# different actions to be taken per implementation. Preference is given first
+# to ${implementation}_${var}, then mpi_${var} and finally defaults will be
+# used. All variables also allow "mpi_none", which disables that action.
+#
+# *_conf_cmd: configure command, default: econf
+# *_conf_args: configure arguments, no default
+# HOWEVER, note that prefix, mandir, infodir and datadir are
+# set if ${S}/configure is executable. Pass "mpi_none" to
+# disable this.
+# *_make_cmd: make command, default emake
+# *_make_args: make arguments, no default
+# *_make_install_cmd: make install command, default emake
+# *_make_install_args: make install arguments, default 'DESTDIR=${D} install'
+
+
+
+# mpi_do_config: $S should be set correctly to some ${P}-${imp}. Changes to
+# that dir, calls mpi_set_env, $conf_cmd $conf_args, and
+# rcalls mpi_restore_env.
+
+# mpi_do_make: Same as above but for building.
+# mpi_do_make_install: Same as above but for installing.
+
+
+inherit multilib flag-o-matic
+
+MPI_EMPI_COMPAT="openmpi-1.2.5-r1 lam-mpi-7.1.4-r1"
+MPI_ALL_IMPS="mpich mpich2 openmpi lam-mpi"
+
+#TODO: doc
+mpi_pkg_deplist() {
+ local i ver
+ if [ -z "$(get_imp)" ]; then
+ ver="virtual/mpi"
+ else
+ for i in ${MPI_EMPI_COMPAT}; do
+ ver="${ver} >=${CATEGORY}/${i}"
+ done
+ ver="|| (${ver} ) app-admin/eselect-mpi"
+ fi
+ echo "${ver}"
+}
+
+mpi_imp_deplist() {
+ local i ver
+ if ! is_empi_imp_build; then
+ for i in ${MPI_ALL_IMPS}; do
+ [ "${i}" != "${PN}" ] && ver="${ver} !sys-cluster/${i}"
+ done
+ else
+ ver="app-admin/eselect-mpi"
+ fi
+ echo "${ver}"
+}
+
+is_imp_build() { [[ ${MPI_ALL_IMPS} == *${PN}* ]]; }
+is_empi_build() { [[ ${CATEGORY} == mpi-* ]]; }
+is_empi_imp_build() { is_imp_build && is_empi_build; }
+
+is_imp() {
+ local i
+ for i in $(eselect mpi list -p); do
+ [[ ${1} == ${i} ]] && return 0
+ done
+ return 1
+}
+
+get_imp() {
+ [[ ${CATEGORY} == mpi-* ]] && echo "${CATEGORY}"
+}
+
+get_mpi_dir() {
+ if is_imp ${CATEGORY} || is_empi_imp_build; then
+ echo "/usr/$(get_libdir)/mpi/${MPI_IMP}"
+ fi
+}
+
+get_eselect_var() { echo "$(eselect mpi printvar ${MPI_IMP} ${1})"; }
+mpi_built_with() { echo "$(get_eselect_var MPI_BUILT_WITH)"; }
+
+# Internal use: Get out of messy functions if we're not using empi to build and
+# therefore avoid tons of file collisions.
+bail_if_not_empi() { [ -z "${MPI_IMP}" ] && return 0; }
+
+#TODO: There must be a better way?
+# Currently can be turned off with mpi_env="mpi_none"
+mpi_set_env() {
+ local p
+ [ -z "${MPI_IMP}" ] && return 0
+ is_empi_imp_build && return 0
+ [[ ${mpi_env} == mpi_none ]] && return 0
+
+ p="$(get_mpi_dir)"
+
+ oCC=$CC
+ oCXX=$CXX
+ oF77=$F77
+ oFC=$FC
+ oPATH=$PATH
+ oLLP=${LD_LIBRARY_PATH}
+ export CC=$(get_eselect_var MPI_CC)
+ export CXX=$(get_eselect_var MPI_CXX)
+ export F77=$(get_eselect_var MPI_F77)
+ export FC=$(get_eselect_var MPI_F90)
+ export PATH="$(get_eselect_var PATH):${PATH}"
+ export LD_LIBRARY_PATH="$(get_eselect_var LD_LIBRARY_PATH):${LD_LIBRARY_PATH}"
+# Handled by the wrappers, at least it better be.
+# append-ldflags $(eselect mpi ldflags ${MPI_IMP})
+# append-flags $(eselect mpi cflags ${MPI_IMP})
+}
+
+mpi_restore_env() {
+ [ -z "${MPI_IMP}" ] && return 0
+ is_empi_imp_build && return 0
+ [[ ${mpi_env} == mpi_none ]] && return 0
+
+ export CC=$oCC
+ export CXX=$oCXX
+ export F77=$oF77
+ export FC=$oFC
+ export PATH=$oPATH
+ export LD_LIBRARY_PATH=$oLLP
+}
+
+
+# Here's what we try to get, in order.
+# ${IMP_BUILT_WITH}_${var}
+# mpi_${var}
+get_mpi_var() {
+ local varname=${1}
+ local t ret
+
+ if is_imp_build; then
+ t="${PN}_${varname}"
+ elif is_empi_build; then
+ t=$(mpi_built_with)
+ t=${t%%-[0-9]*}
+ t="${t}_${varname}"
+ fi
+ [ -n "${t}" ] && ret="${!t}"
+
+ if [ -z "${ret}" ]; then
+ t="mpi_${varname}"
+ ret=${!t}
+ fi
+
+ if [ -z "${ret}" ]; then
+ case ${varname} in
+ conf_cmd)
+ ret="econf"
+ ;;
+ make_cmd|make_install_cmd)
+ ret="emake"
+ ;;
+ esac
+ fi
+ echo "${ret}"
+}
+
+mpi_do_config() {
+ local conf_cmd=$(get_mpi_var "conf_cmd")
+ local conf_args=$(get_mpi_var "conf_args")
+ local default_args rc d
+
+ d="$(get_mpi_dir)"
+ [[ "${conf_cmd}" == "mpi_none" ]] && return 0
+ [[ -x ${S}/configure && -n "${MPI_IMP}" ]] \
+ && default_args="--prefix=${d}/usr/
+ --mandir=${d}/usr/share/man
+ --infodir=${d}/usr/share/info
+ --datadir=${d}/usr/share/
+ --sysconfdir=/etc/${MPI_IMP}/
+ --localstatedir=/var/lib/${MPI_IMP}"
+ [[ "${conf_args}" == *mpi_none* ]] && default_args=""
+
+ mpi_set_env
+ ${conf_cmd} ${default_args} ${conf_args}; rc=$?
+ mpi_restore_env
+ return ${rc}
+}
+
+mpi_do_make() {
+ local make_cmd=$(get_mpi_var "make_cmd")
+ local make_args=$(get_mpi_var "make_args")
+ local rc
+
+ [[ "${make_cmd}" == "mpi_none" ]] && return 0
+
+ mpi_set_env
+ ${make_cmd} ${make_args}; rc=$?
+ mpi_restore_env
+ return ${rc}
+}
+
+
+mpi_do_make_install() {
+ local make_cmd=$(get_mpi_var "make_install_cmd")
+ local make_args=$(get_mpi_var "make_install_args")
+ local default_args="DESTDIR=\"${D}\" install"
+ local rc
+
+ [[ "${make_cmd}" == "mpi_none" ]] && return 0
+ [[ "${make_args}" == "mpi_none" ]] && default_args=""
+
+ mpi_set_env
+ ${make_cmd} ${default_args} ${make_args}; rc=$?
+ mpi_restore_env
+ return ${rc}
+}
+
+mpi_src_compile() {
+ # Be nice and check at the earliest moment so the user doesn't watch
+ # everything compile only to have the emerge blow up.
+ if is_empi_imp_build && [ ! -f "${FILESDIR}"/${MPI_ESELECT_FILE} ]; then
+ die "MPI_ESELECT_FILE is not defined/found. ${MPI_ESELECT_FILE}"
+ fi
+
+ pushd "${S}" &>/dev/null
+ mpi_do_config || die "mpi_src_compile: mpi_do_config failed."
+ mpi_do_make || die "mpi_src_compile: mpi_do_make failed."
+ popd &>/dev/null
+}
+
+mpi_src_install() {
+ pushd "${S}" &>/dev/null
+ mpi_do_make_install \
+ || die "mpi_src_install(${MPI_IMP}) mpi_do_make_install failed."
+ popd &>/dev/null
+
+ [ -z "${MPI_IMP}" ] && return 0
+ if is_empi_imp_build; then
+ mpi_add_eselect
+ fi
+}
+
+mpi_pkg_setup() {
+ # Make sure this eclass should be used.
+ MPI_IMP=$(get_imp)
+ [ -z "${MPI_IMP}" ] && return 0
+
+ if [[ -z ${MPI_IMP} ]]; then
+ die "Building without empi and bail_if_not_empi failed."
+ fi
+
+ if ! is_empi_imp_build; then
+ einfo "mpi: Building against implementation ${MPI_IMP}."
+ fi
+}
+
+mpi_add_eselect() {
+ cp "${FILESDIR}"/${MPI_ESELECT_FILE} ${T}/${MPI_IMP}.eselect || die
+ sed -i \
+ -e "s|@ROOT@|$(get_mpi_dir)|g" \
+ -e "s|@LIBDIR@|$(get_libdir)|g" \
+ -e "s|@BUILT_WITH@|${PF}|g" \
+ ${T}/${MPI_IMP}.eselect
+
+ eselect mpi add "${T}"/${MPI_IMP}.eselect
+}
+
+
+
+# Handles all the mpi_{do,new} functions below.
+# Not handled because there is no good way:
+# doconfd doenvd domo doinitd
+mpi_do() {
+ local rc prefix
+ local cmd=${1}
+ local ran=1
+ local slash=/
+ local mdir="$(get_mpi_dir)/"
+
+ if ! is_empi_build; then
+ $*
+ return ${?}
+ fi
+
+ shift
+ if [ "${cmd#do}" != "${cmd}" ]; then
+ prefix="do"; cmd=${cmd#do}
+ elif [ "${cmd#new}" != "${cmd}" ]; then
+ prefix="new"; cmd=${cmd#new}
+ else
+ die "Unknown command passed to mpi_do: ${cmd}"
+ fi
+ case ${cmd} in
+ bin|lib|lib.a|lib.so|sbin)
+ DESTTREE="${mdir}usr" ${prefix}${cmd} $*
+ rc=$?;;
+ doc)
+ _E_DOCDESTTREE_="../../../../${mdir}usr/share/doc/${PF}/${_E_DOCDESTTREE_}" \
+ ${prefix}${cmd} $*
+ rc=$?;;
+ html)
+ _E_DOCDESTTREE_="../../../../${mdir}usr/share/doc/${PF}/www/${_E_DOCDESTTREE_}" \
+ ${prefix}${cmd} $*
+ rc=$?;;
+ exe)
+ _E_EXEDESTTREE_="${mdir}${_E_EXEDESTTREE_}" ${prefix}${cmd} $*
+ rc=$?;;
+ man|info)
+ [ -d "${D}"usr/share/${cmd} ] && mv "${D}"usr/share/${cmd}{,-orig}
+ [ ! -d "${D}"${mdir}usr/share/${cmd} ] \
+ && install -d "${D}"${mdir}usr/share/${cmd}
+
+ ln -snf ../../${mdir}usr/share/${cmd} ${D}usr/share/${cmd}
+ ${prefix}${cmd} $*
+ rc=$?
+ rm "${D}"usr/share/${cmd}
+ [ -d "${D}"usr/share/${cmd}-orig ] && mv "${D}"usr/share/${cmd}{-orig,}
+ ;;
+ dir)
+ dodir "${@/#${slash}/${mdir}${slash}}"; rc=$?;;
+ hard|sym)
+ ${prefix}${cmd} "${mdir}$1" "${mdir}/$2"; rc=$?;;
+ ins)
+ INSDESTTREE="${mdir}${INSTREE}" ${cmd}${prefix} $*; rc=$?;;
+ *)
+ rc=0;;
+ esac
+
+ [[ ${ran} -eq 0 ]] && die "mpi_do passed unknown command: ${cmd}"
+ return ${rc}
+}
+
+mpi_dobin() { mpi_do "dodoc" $*; }
+mpi_newbin() { mpi_do "newdoc" $*; }
+mpi_dodoc() { mpi_do "dodoc" $*; }
+mpi_newdoc() { mpi_do "newdoc" $*; }
+mpi_doexe() { mpi_do "doexe" $*; }
+mpi_newexe() { mpi_do "newexe" $*; }
+mpi_dohtml() { mpi_do "dohtml" $*; }
+mpi_dolib() { mpi_do "dolib" $*; }
+mpi_dolib.a() { mpi_do "dolib.a" $*; }
+mpi_newlib.a() { mpi_do "newlib.a" $*; }
+mpi_dolib.so() { mpi_do "dolib.so" $*; }
+mpi_newlib.so() { mpi_do "newlib.so" $*; }
+mpi_dosbin() { mpi_do "dosbin" $*; }
+mpi_newsbin() { mpi_do "newsbin" $*; }
+mpi_doman() { mpi_do "doman" $*; }
+mpi_newman() { mpi_do "newman" $*; }
+mpi_doinfo() { mpi_do "doinfo" $*; }
+mpi_dodir() { mpi_do "dodir" $*; }
+mpi_dohard() { mpi_do "dohard" $*; }
+mpi_doins() { mpi_do "doins" $*; }
+mpi_dosym() { mpi_do "dosym" $*; }
+
+EXPORT_FUNCTIONS src_compile src_install pkg_setup
diff --git a/eclass/octave-forge.eclass b/eclass/octave-forge.eclass
new file mode 100644
index 000000000..d0ca6eab0
--- /dev/null
+++ b/eclass/octave-forge.eclass
@@ -0,0 +1,394 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header
+
+#
+# Version: 0.08 (2008-02-23)
+# Authors: Markus Dittrich <markusle@gentoo.org>
+#
+# The octave-forge eclass installs and manages the split
+# octave-forge packages. In a nutshell, it does two things:
+# 1) Compile (if necessary) and install individual octave-forge
+# packages
+# 2) Add/Remove the octave-forge package and its description
+# from the database file in
+# /usr/share/octave/octave_packages
+# such that octave knows what octave-forge packages are
+# installed and what functionality they provide.
+#
+# The individual octave-forge packages should only need to inherit
+# this eclass and possible have some additional dependencies and/or
+# custom patches.
+#
+
+HOMEPAGE="http://octave.sourceforge.net"
+SLOT="0"
+LICENSE="GPL-2"
+
+EXPORT_FUNCTIONS src_compile src_install pkg_postinst pkg_prerm
+
+# unless requested otherwise we're happy with octave-3.0.0
+NEED_OCTAVE=${NEED_OCTAVE:-3.0.0}
+
+DEPEND="${DEPEND}
+ >=sci-mathematics/octave-${NEED_OCTAVE}
+ || ( >=sys-apps/coreutils-6.10-r1 sys-apps/mktemp )"
+RDEPEND="${RDEPEND}
+ >=sci-mathematics/octave-${NEED_OCTAVE}"
+
+
+#################################################################
+# define global paths needed for the install
+#################################################################
+OCT_PKG=${P#octave-forge-}
+OCT_PKG_NAME=${PN#octave-forge-}
+OCT_INSTALL_ROOT=/usr/share/octave
+OCT_INSTALL_PKG="${OCT_INSTALL_ROOT}/packages/${OCT_PKG}"
+OCT_BINARY=$(type -p octave)
+OCT_DATABASE="${OCT_INSTALL_ROOT}/octave_packages"
+OCT_DESC="${OCT_INSTALL_PKG}/packinfo/DESCRIPTION"
+S="${WORKDIR}/${OCT_PKG}"
+OCT_DESC_SRC="${S}/DESCRIPTION"
+
+
+################################################################
+# generate the name of the architecture dependend install
+# directory for binary files (*.mex, *.oct)
+################################################################
+octave_getarch() {
+ local host_type="$(octave-config -p CANONICAL_HOST_TYPE)";
+ eval $1="${host_type}-$(octave-config -p API_VERSION)";
+}
+
+
+#################################################################
+# determine if autoload is requested
+#################################################################
+check_autoload() {
+ local answer="$(fgrep -i 'autoload' "${OCT_DESC_SRC}" | cut -d' ' -f2)"
+ if [[ "${answer}" == "yes" \
+ || "${answer}" == "true" \
+ || "${answer}" == "0" \
+ || "${answer}" == "1" ]]; then
+ eval $1="${answer}"
+ fi
+}
+
+#################################################################
+# extract package description from the DESCRIPTION file into
+# an array so we can use it later to update the octave database
+#################################################################
+get_description()
+{
+ local count=0
+ local tracker=0
+ local line
+ while read line
+ do
+ if [[ "${line}" == *:* ]]; then
+ keys[${count}]=$(echo "${line}" | cut -f1 -d: | sed -e "s: $::g" | gawk '{ print tolower($1)}')
+ values[${count}]=$(echo "${line}" | cut -f2 -d: | sed -e "s:^ ::g")
+ if [[ ${keys[count]} == "depends" ]]; then
+ tracker=${count}
+ fi
+
+ (( count++ ))
+ fi
+ done < "${OCT_DESC}"
+
+ # further separate depend string
+ local depend_value=${values[tracker]}
+ depend_value=${depend_value/\(/}
+ depend_value=${depend_value/\)/}
+ pkg_name=$(echo ${depend_value} | cut -d' ' -f1)
+ operator=$(echo ${depend_value} | cut -d' ' -f2)
+ version=$(echo ${depend_value} | cut -d' ' -f3)
+}
+
+
+################################################################
+# this function reads the DESCRIPTION file into a bash array,
+# then uses the latter to generate a temporary octave file and
+# finally calls octave on the temporary file to update the
+# database
+################################################################
+add_pkg_to_database()
+{
+ # read properties from DESCRIPTION file
+ declare -a keys
+ declare -a values
+ get_description
+
+ # securely generate tmp file
+ OCT_TMP=$(mktemp generate-database.XXXXXXXXXX) \
+ || die "Failed to generate temporary file."
+
+ if [ -e "${OCT_DATABASE}" ]; then
+ echo "global_packages = load (\"${OCT_DATABASE}\").global_packages;" >> "${OCT_TMP}"
+ else
+ echo "global_packages = {};" >> "${OCT_TMP}"
+ fi
+
+ echo "new_package = struct();" >> "${OCT_TMP}"
+
+ # path to parent of directory holding mex/oct files
+ local libexec_dir="${OCT_INSTALL_PKG}"
+ echo "new_package.archprefix = \"${libexec_dir}\";" \
+ >> "${OCT_TMP}"
+
+ for ((count=0; count < ${#keys[*]}; count++)); do
+ # the depend string needs a separate struct
+ if [[ ${keys[count]} == "depends" ]]; then
+ echo "temp = struct(\"operator\",\"${operator}\",\"package\",\"${pkg_name}\",\"version\",\"${version}\");" >> "${OCT_TMP}"
+ echo "foo = {temp};" >> "${OCT_TMP}"
+ echo "new_package.depends = foo;" >> "${OCT_TMP}"
+ elif [[ ${keys[count]} == "name" ]]; then
+ echo "new_package.${keys[count]} = lower(\"${values[count]}\");" >> "${OCT_TMP}"
+ else
+ echo "new_package.${keys[count]} = \"${values[count]}\";" >> "${OCT_TMP}"
+ fi
+ done
+
+ cat >> "${OCT_TMP}" <<-EOF
+ new_package.dir = "${OCT_INSTALL_PKG}";
+ global_packages = { global_packages{:}, new_package};
+ save("${OCT_DATABASE}","global_packages");
+ EOF
+
+ # let octave do the final setup of the database file
+ echo
+ ebegin "Adding package to global octave database."
+ "${OCT_BINARY}" -q "${OCT_TMP}" >& /dev/null
+ eend $?
+ echo;
+
+ # remove the temporary octave file
+ rm -f "${OCT_TMP}" \
+ || die "Failed to remove temporary octave database code."
+}
+
+
+#################################################################
+# this function removes an octave-forge package from the
+# to global package database
+#################################################################
+delete_pkg_from_database()
+{
+ # read properties from DESCRIPTION file
+ declare -a keys
+ declare -a values
+ get_description
+
+ local remove_name
+ for ((count=0; count < ${#keys[*]}; count++)); do
+ if [[ ${keys[count]} == "name" ]]; then
+ remove_name=${values[count]}
+ fi
+ done
+
+ # securely generate tmp file
+ OCT_TMP=$(mktemp /tmp/generate-database.XXXXXXXXXX) || \
+ die "Failed to generate temporary file."
+
+ # generate octave code to remove relevant entry from
+ # global file
+ cat >> "${OCT_TMP}" <<-EOF
+ old_packages = load ("${OCT_DATABASE}").global_packages;
+ global_packages = {};
+ purge_name = lower("${remove_name}");
+ for i=1:length(old_packages);
+ if ( !strcmp(old_packages{i}.name,purge_name));
+ global_packages = {global_packages{:}, old_packages{i}}; endif; endfor;
+ save ("${OCT_DATABASE}","global_packages");
+ EOF
+
+ # let octave do the final setup of the database file
+ echo
+ ebegin "Removing from database"
+ "${OCT_BINARY}" -q "${OCT_TMP}" >& /dev/null
+ eend $?
+
+ # if the database file is empty we get rid of it completely
+ # otherwise octave will be confused. To do so, we simply
+ # check if there are any author fields left.
+ fgrep 'author' "${OCT_DATABASE}" >& /dev/null
+ if [[ $? == 1 ]]; then
+ ebegin "Purging empty database"
+ rm -f "${OCT_DATABASE}"
+ eend $?
+ fi
+ echo
+
+ # remove the temporary octave file
+ rm -f "${OCT_TMP}" \
+ || die "Failed to remove temporary octave database code."
+}
+
+
+#################################################################
+# our custom src_compile tries to do the Right Thing for each
+# of the individual octave-forge packages. Some require
+# compilation via configure/make, make only, and some simply
+# install several *.m files without any compilation at all.
+#################################################################
+octave-forge_src_compile() {
+ cd "${S}"
+
+ # check for configure/makefile since not all octave-forge
+ # packages have one
+ if [[ -e src/configure ]]; then
+ pushd . && cd src/
+ econf || die "configure failed in src"
+ popd
+ fi
+
+ if [[ -e src/Makefile ]]; then
+ pushd . && cd src/
+ emake -j1 || die "make failed in src"
+ popd
+ fi
+
+ # we need to check if there are any examples
+ # to build as well
+ if [[ -e examples/configure ]]; then
+ pushd . && cd examples/
+ econf || die "configure failed in examples"
+ popd
+ fi
+
+ if [[ -e examples/Makefile ]]; then
+ pushd . && cd examples/
+ emake -j1 || die "make failed in examples"
+ popd
+ fi
+}
+
+
+####################################################################
+# install *.m and *.oct/*.mex files if present into the locations
+# where octave expects them.
+####################################################################
+octave-forge_src_install() {
+ cd "${S}"
+
+ # get arch string
+ local octave_arch=""
+ octave_getarch octave_arch
+
+ # check if we have *.m, *.mex, and *.oct files in src
+ m_files=$(find ./src -type f -name "*.m" -print0 2> /dev/null)
+ oct_files=$(find ./src -type f -name "*.oct" -print0 2> /dev/null)
+ mex_files=$(find ./src -type f -name "*.mex" -print0 2> /dev/null)
+
+ # install *.m files
+ insinto "${OCT_INSTALL_PKG}"
+ if [[ -n "${m_files}" ]]; then
+ doins src/*.m \
+ || die "failed to install m files"
+ fi
+
+ # install *.mex/*.oct files if present
+ if [[ -n "${oct_files}" || -n "${mex_files}" ]]; then
+ insinto "${OCT_INSTALL_PKG}/${octave_arch}"
+ if [[ -n "${oct_files}" ]]; then
+ doins src/*.oct \
+ || die "failed to install oct files"
+ fi
+ if [[ -n "${mex_files}" ]]; then
+ doins src/*.mex \
+ || die "failed to install mex files"
+ fi
+ fi
+
+ # include PKG_ADD and PKG_DEL
+ # TODO: need to scan included *.m *.cc files for
+ # additional PKG_ADD/PKG_DEL commands for appending
+ if [[ -e "${S}/PKG_ADD" ]]; then
+ insinto "${OCT_INSTALL_PKG}"
+ doins "${S}/PKG_ADD" \
+ || die "failed to install PKG_ADD"
+ fi
+ if [[ -e "${S}/PKG_DEL" ]]; then
+ insinto "${OCT_INSTALL_PKG}"
+ doins "${S}/PKG_DEL" \
+ || die "failed to install PKG_ADD"
+ fi
+
+ # copy files in inst if they exits
+ if [[ -d "${S}"/inst ]]; then
+ insinto "${OCT_INSTALL_PKG}"
+ doins inst/* \
+ || die "failed to install inst/"
+ fi
+
+ # check for on_uninstall.m and install if present
+ local uninstall_file=$(find "${S}" -name 'on_uninstall.m')
+ if [[ -n "${uninstall_file}" ]]; then
+ doins "${uninstall_file}" \
+ || die "failed to install on_uninstall.m"
+ fi
+
+ # copy files in packinfo
+ insinto "${OCT_INSTALL_PKG}"/packinfo
+ doins COPYING DESCRIPTION \
+ || die "failed to install packinfo files"
+
+ # copy Changelog if present
+ if [[ -e "Changelog" ]]; then
+ doins Changelog \
+ || die "failed to install Changelog"
+ fi
+
+ # mark package as autoload if requested
+ local want_autoload=""
+ check_autoload want_autoload
+ if [[ -n "${want_autoload}" ]]; then
+ touch "${T}"/.autoload && doins "${T}"/.autoload \
+ || die "failed to install autoload"
+ fi
+
+ # check for index file
+ # TODO: need to generate index file in case it is missing
+ local index_file=$(find "${S}" -name 'INDEX')
+ if [ -n "${index_file}" ]; then
+ doins "${index_file}" \
+ || die "failed to install INDEX"
+ fi
+
+ # check for doc directory and install content if present
+ if [[ -d "${S}"/doc ]]; then
+ insinto "${OCT_INSTALL_PKG}"/doc
+ doins doc/* \
+ || die "failed to install docs"
+ fi
+
+ # check for bin directory and install content if present
+ if [[ -d "${S}"/bin ]]; then
+ insinto "${OCT_INSTALL_PKG}"/bin
+ doins bin/* \
+ || die "failed to install bin"
+ fi
+
+ # check for examples to be installed
+ if [[ -d "${S}"/examples ]]; then
+ insinto "${OCT_INSTALL_PKG}"/examples
+ doins examples/*.m examples/*.oct examples/README \
+ || die "failed to install example files"
+ fi
+}
+
+
+##################################################################
+# after installing add package to global octave database
+##################################################################
+octave-forge_pkg_postinst() {
+ add_pkg_to_database
+}
+
+
+##################################################################
+# after unmerging remove package from global octave database
+##################################################################
+octave-forge_pkg_prerm() {
+ delete_pkg_from_database
+}
diff --git a/licenses/NOSA b/licenses/NOSA
new file mode 100644
index 000000000..298f1e588
--- /dev/null
+++ b/licenses/NOSA
@@ -0,0 +1,258 @@
+NASA OPEN SOURCE AGREEMENT VERSION 1.3
+
+THIS OPEN SOURCE AGREEMENT ("AGREEMENT") DEFINES THE RIGHTS OF USE,
+REPRODUCTION, DISTRIBUTION, MODIFICATION AND REDISTRIBUTION OF CERTAIN
+COMPUTER SOFTWARE ORIGINALLY RELEASED BY THE UNITED STATES GOVERNMENT
+AS REPRESENTED BY THE GOVERNMENT AGENCY LISTED BELOW ("GOVERNMENT
+AGENCY"). THE UNITED STATES GOVERNMENT, AS REPRESENTED BY GOVERNMENT
+AGENCY, IS AN INTENDED THIRD-PARTY BENEFICIARY OF ALL SUBSEQUENT
+DISTRIBUTIONS OR REDISTRIBUTIONS OF THE SUBJECT SOFTWARE. ANYONE WHO
+USES, REPRODUCES, DISTRIBUTES, MODIFIES OR REDISTRIBUTES THE SUBJECT
+SOFTWARE, AS DEFINED HEREIN, OR ANY PART THEREOF, IS, BY THAT ACTION,
+ACCEPTING IN FULL THE RESPONSIBILITIES AND OBLIGATIONS CONTAINED IN
+THIS AGREEMENT.
+
+Government Agency: National Aeronautics and Space Administration (NASA)
+Government Agency Original Software Designation: ARC-15277
+Government Agency Original Software Title: growler 0.1
+User Registration Requested. Please Visit http://opensource.arc.nasa.gov/
+Government Agency Point of Contact for Original Software: bgreen@nas.nasa.gov
+
+1. DEFINITIONS
+
+A. "Contributor" means Government Agency, as the developer of the
+Original Software, and any entity that makes a Modification.
+
+B. "Covered Patents" mean patent claims licensable by a Contributor
+that are necessarily infringed by the use or sale of its Modification
+alone or when combined with the Subject Software.
+
+C. "Display" means the showing of a copy of the Subject Software,
+either directly or by means of an image, or any other device.
+
+D. "Distribution" means conveyance or transfer of the Subject
+Software, regardless of means, to another.
+
+E. "Larger Work" means computer software that combines Subject
+Software, or portions thereof, with software separate from the Subject
+Software that is not governed by the terms of this Agreement.
+
+F. "Modification" means any alteration of, including addition to or
+deletion from, the substance or structure of either the Original
+Software or Subject Software, and includes derivative works, as that
+term is defined in the Copyright Statute, 17 USC 101. However, the
+act of including Subject Software as part of a Larger Work does not in
+and of itself constitute a Modification.
+
+G. "Original Software" means the computer software first released
+under this Agreement by Government Agency with Government Agency
+designation ARC-15277 and entitled growler, including source code,
+object code and accompanying documentation, if any.
+
+H. "Recipient" means anyone who acquires the Subject Software under
+this Agreement, including all Contributors.
+
+I. "Redistribution" means Distribution of the Subject Software after a
+Modification has been made.
+
+J. "Reproduction" means the making of a counterpart, image or copy of
+the Subject Software.
+
+K. "Sale" means the exchange of the Subject Software for money or
+equivalent value.
+
+L. "Subject Software" means the Original Software, Modifications, or
+any respective parts thereof.
+
+M. "Use" means the application or employment of the Subject Software
+for any purpose.
+
+2. GRANT OF RIGHTS
+
+A. Under Non-Patent Rights: Subject to the terms and conditions of
+this Agreement, each Contributor, with respect to its own contribution
+to the Subject Software, hereby grants to each Recipient a
+non-exclusive, world-wide, royalty-free license to engage in the
+following activities pertaining to the Subject Software:
+
+1. Use
+2. Distribution
+3. Reproduction
+4. Modification
+5. Redistribution
+6. Display
+
+B. Under Patent Rights: Subject to the terms and conditions of this
+Agreement, each Contributor, with respect to its own contribution to
+the Subject Software, hereby grants to each Recipient under Covered
+Patents a non-exclusive, world-wide, royalty-free license to engage in
+the following activities pertaining to the Subject Software:
+
+1. Use
+2. Distribution
+3. Reproduction
+4. Sale
+5. Offer for Sale
+
+C. The rights granted under Paragraph B. also apply to the combination
+of a Contributor's Modification and the Subject Software if, at the
+time the Modification is added by the Contributor, the addition of
+such Modification causes the combination to be covered by the Covered
+Patents. It does not apply to any other combinations that include a
+Modification.
+
+D. The rights granted in Paragraphs A. and B. allow the Recipient to
+sublicense those same rights. Such sublicense must be under the same
+terms and conditions of this Agreement.
+
+3. OBLIGATIONS OF RECIPIENT
+
+A. Distribution or Redistribution of the Subject Software must be made
+under this Agreement except for additions covered under paragraph 3H.
+
+1. Whenever a Recipient distributes or redistributes the Subject
+ Software, a copy of this Agreement must be included with each copy
+ of the Subject Software; and
+2. If Recipient distributes or redistributes the Subject Software in
+ any form other than source code, Recipient must also make the
+ source code freely available, and must provide with each copy of
+ the Subject Software information on how to obtain the source code
+ in a reasonable manner on or through a medium customarily used for
+ software exchange.
+
+B. Each Recipient must ensure that the following copyright notice
+appears prominently in the Subject Software:
+
+Copyright ã 2004 United States Government as represented by the
+Administrator of the National Aeronautics and Space Administration.
+All Rights Reserved.
+
+C. Each Contributor must characterize its alteration of the Subject
+Software as a Modification and must identify itself as the originator
+of its Modification in a manner that reasonably allows subsequent
+Recipients to identify the originator of the Modification. In
+fulfillment of these requirements, Contributor must include a file
+(e.g., a change log file) that describes the alterations made and the
+date of the alterations, identifies Contributor as originator of the
+alterations, and consents to characterization of the alterations as a
+Modification, for example, by including a statement that the
+Modification is derived, directly or indirectly, from Original
+Software provided by Government Agency. Once consent is granted, it
+may not thereafter be revoked.
+
+D. A Contributor may add its own copyright notice to the Subject
+Software. Once a copyright notice has been added to the Subject
+Software, a Recipient may not remove it without the express permission
+of the Contributor who added the notice.
+
+E. A Recipient may not make any representation in the Subject Software
+or in any promotional, advertising or other material that may be
+construed as an endorsement by Government Agency or by any prior
+Recipient of any product or service provided by Recipient, or that may
+seek to obtain commercial advantage by the fact of Government Agency's
+or a prior Recipient's participation in this Agreement.
+
+F. In an effort to track usage and maintain accurate records of the
+Subject Software, each Recipient, upon receipt of the Subject
+Software, is requested to register with Government Agency by visiting
+the following website: http://opensource.arc.nasa.gov. Recipient's
+name and personal information shall be used for statistical purposes
+only. Once a Recipient makes a Modification available, it is requested
+that the Recipient inform Government Agency at the web site provided
+above how to access the Modification.
+
+G. Each Contributor represents that that its Modification is believed
+to be Contributor's original creation and does not violate any
+existing agreements, regulations, statutes or rules, and further that
+Contributor has sufficient rights to grant the rights conveyed by this
+Agreement.
+
+H. A Recipient may choose to offer, and to charge a fee for, warranty,
+support, indemnity and/or liability obligations to one or more other
+Recipients of the Subject Software. A Recipient may do so, however,
+only on its own behalf and not on behalf of Government Agency or any
+other Recipient. Such a Recipient must make it absolutely clear that
+any such warranty, support, indemnity and/or liability obligation is
+offered by that Recipient alone. Further, such Recipient agrees to
+indemnify Government Agency and every other Recipient for any
+liability incurred by them as a result of warranty, support, indemnity
+and/or liability offered by such Recipient.
+
+I. A Recipient may create a Larger Work by combining Subject Software
+with separate software not governed by the terms of this agreement and
+distribute the Larger Work as a single product. In such case, the
+Recipient must make sure Subject Software, or portions thereof,
+included in the Larger Work is subject to this Agreement.
+
+J. Notwithstanding any provisions contained herein, Recipient is
+hereby put on notice that export of any goods or technical data from
+the United States may require some form of export license from the
+U.S. Government. Failure to obtain necessary export licenses may
+result in criminal liability under U.S. laws. Government Agency
+neither represents that a license shall not be required nor that, if
+required, it shall be issued. Nothing granted herein provides any
+such export license.
+
+4. DISCLAIMER OF WARRANTIES AND LIABILITIES; WAIVER AND INDEMNIFICATION
+
+A. No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY
+WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY,
+INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE
+WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM
+INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR
+FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO
+THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER,
+CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT
+OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY
+OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.
+FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES
+REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE,
+AND DISTRIBUTES IT "AS IS."
+
+B. Waiver and Indemnity: RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS
+AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND
+SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT. IF RECIPIENT'S USE OF
+THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES,
+EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM
+PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT
+SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED
+STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY
+PRIOR RECIPIENT, TO THE EXTENT PERMITTED BY LAW. RECIPIENT'S SOLE
+REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL
+TERMINATION OF THIS AGREEMENT.
+
+
+5. GENERAL TERMS
+
+A. Termination: This Agreement and the rights granted hereunder will
+terminate automatically if a Recipient fails to comply with these
+terms and conditions, and fails to cure such noncompliance within
+thirty (30) days of becoming aware of such noncompliance. Upon
+termination, a Recipient agrees to immediately cease use and
+distribution of the Subject Software. All sublicenses to the Subject
+Software properly granted by the breaching Recipient shall survive any
+such termination of this Agreement.
+
+B. Severability: If any provision of this Agreement is invalid or
+unenforceable under applicable law, it shall not affect the validity
+or enforceability of the remainder of the terms of this Agreement.
+
+C. Applicable Law: This Agreement shall be subject to United States
+federal law only for all purposes, including, but not limited to,
+determining the validity of this Agreement, the meaning of its
+provisions and the rights, obligations and remedies of the parties.
+
+D. Entire Understanding: This Agreement constitutes the entire
+understanding and agreement of the parties relating to release of the
+Subject Software and may not be superseded, modified or amended except
+by further written agreement duly executed by the parties.
+
+E. Binding Authority: By accepting and using the Subject Software
+under this Agreement, a Recipient affirms its authority to bind the
+Recipient to all terms and conditions of this Agreement and that that
+Recipient hereby agrees to all terms and conditions herein.
+
+F. Point of Contact: Any Recipient contact with Government Agency is
+to be directed to the designated representative as follows:
+bgreen@nas.nasa.gov.
diff --git a/licenses/OSL-2.1 b/licenses/OSL-2.1
new file mode 100644
index 000000000..12eace30f
--- /dev/null
+++ b/licenses/OSL-2.1
@@ -0,0 +1,155 @@
+Open Software License v. 2.1
+============================
+This Open Software License (the "License") applies to any original work
+of authorship (the "Original Work") whose owner (the "Licensor") has
+placed the following notice immediately following the copyright notice
+for the Original Work: Licensed under the Open Software License version 2.1
+
+1) Grant of Copyright License. Licensor hereby grants You a world-wide,
+royalty-free, non-exclusive, perpetual, sublicenseable license to do
+the following:
+
+to reproduce the Original Work in copies;
+to prepare derivative works ("Derivative Works") based upon the Original Work;
+to distribute copies of the Original Work and Derivative Works to the
+ public, with the proviso that copies of Original Work or Derivative Works
+ that You distribute shall be licensed under the Open Software License;
+to perform the Original Work publicly; and
+to display the Original Work publicly.
+
+2) Grant of Patent License. Licensor hereby grants You a world-wide,
+royalty-free, non-exclusive, perpetual, sublicenseable license, under
+patent claims owned or controlled by the Licensor that are embodied in
+the Original Work as furnished by the Licensor, to make, use, sell and
+offer for sale the Original Work and Derivative Works.
+
+3) Grant of Source Code License. The term "Source Code" means the
+preferred form of the Original Work for making modifications to it
+and all available documentation describing how to modify the Original
+Work. Licensor hereby agrees to provide a machine-readable copy of the
+Source Code of the Original Work along with each copy of the Original
+Work that Licensor distributes. Licensor reserves the right to satisfy
+this obligation by placing a machine-readable copy of the Source Code in
+an information repository reasonably calculated to permit inexpensive and
+convenient access by You for as long as Licensor continues to distribute
+the Original Work, and by publishing the address of that information
+repository in a notice immediately following the copyright notice that
+applies to the Original Work.
+
+4) Exclusions From License Grant. Neither the names of Licensor, nor
+the names of any contributors to the Original Work, nor any of their
+trademarks or service marks, may be used to endorse or promote products
+derived from this Original Work without express prior written permission
+of the Licensor. Nothing in this License shall be deemed to grant any
+rights to trademarks, copyrights, patents, trade secrets or any other
+intellectual property of Licensor except as expressly stated herein. No
+patent license is granted to make, use, sell or offer to sell embodiments
+of any patent claims other than the licensed claims defined in Section
+2. No right is granted to the trademarks of Licensor even if such marks
+are included in the Original Work. Nothing in this License shall be
+interpreted to prohibit Licensor from licensing under different terms
+from this License any Original Work that Licensor otherwise would have
+a right to license.
+
+5) External Deployment. The term "External Deployment" means the use or
+distribution of the Original Work or Derivative Works in any way such that
+the Original Work or Derivative Works may be used by anyone other than
+You, whether the Original Work or Derivative Works are distributed to
+those persons or made available as an application intended for use over
+a computer network. As an express condition for the grants of license
+hereunder, You agree that any External Deployment by You of a Derivative
+Work shall be deemed a distribution and shall be licensed to all under
+the terms of this License, as prescribed in section 1(c) herein.
+
+6) Attribution Rights. You must retain, in the Source Code of any
+Derivative Works that You create, all copyright, patent or trademark
+notices from the Source Code of the Original Work, as well as any
+notices of licensing and any descriptive text identified therein as an
+"Attribution Notice." You must cause the Source Code for any Derivative
+Works that You create to carry a prominent Attribution Notice reasonably
+calculated to inform recipients that You have modified the Original Work.
+
+7) Warranty of Provenance and Disclaimer of Warranty. Licensor
+warrants that the copyright in and to the Original Work and the patent
+rights granted herein by Licensor are owned by the Licensor or are
+sublicensed to You under the terms of this License with the permission
+of the contributor(s) of those copyrights and patent rights. Except as
+expressly stated in the immediately proceeding sentence, the Original
+Work is provided under this License on an "AS IS" BASIS and WITHOUT
+WARRANTY, either express or implied, including, without limitation,
+the warranties of NON-INFRINGEMENT, MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF THE ORIGINAL
+WORK IS WITH YOU. This DISCLAIMER OF WARRANTY constitutes an essential
+part of this License. No license to Original Work is granted hereunder
+except under this disclaimer.
+
+8) Limitation of Liability. Under no circumstances and under no legal
+theory, whether in tort (including negligence), contract, or otherwise,
+shall the Licensor be liable to any person for any direct, indirect,
+special, incidental, or consequential damages of any character arising
+as a result of this License or the use of the Original Work including,
+without limitation, damages for loss of goodwill, work stoppage, computer
+failure or malfunction, or any and all other commercial damages or
+losses. This limitation of liability shall not apply to liability for
+death or personal injury resulting from Licensor's negligence to the
+extent applicable law prohibits such limitation. Some jurisdictions do
+not allow the exclusion or limitation of incidental or consequential
+damages, so this exclusion and limitation may not apply to You.
+
+9) Acceptance and Termination. If You distribute copies of the Original
+Work or a Derivative Work, You must make a reasonable effort under the
+circumstances to obtain the express assent of recipients to the terms of
+this License. Nothing else but this License (or another written agreement
+between Licensor and You) grants You permission to create Derivative Works
+based upon the Original Work or to exercise any of the rights granted
+in Section 1 herein, and any attempt to do so except under the terms of
+this License (or another written agreement between Licensor and You)
+is expressly prohibited by U.S. copyright law, the equivalent laws of
+other countries, and by international treaty. Therefore, by exercising
+any of the rights granted to You in Section 1 herein, You indicate Your
+acceptance of this License and all of its terms and conditions. This
+License shall terminate immediately and you may no longer exercise any
+of the rights granted to You by this License upon Your failure to honor
+the proviso in Section 1(c) herein.
+
+10) Termination for Patent Action. This License shall terminate
+automatically and You may no longer exercise any of the rights granted
+to You by this License as of the date You commence an action, including
+a cross-claim or counterclaim, against Licensor or any licensee alleging
+that the Original Work infringes a patent. This termination provision
+shall not apply for an action alleging patent infringement by combinations
+of the Original Work with other software or hardware.
+
+11) Jurisdiction, Venue and Governing Law. Any action or suit relating to this License may be brought only in the courts of a jurisdiction wherein the Licensor resides or in which Licensor conducts its primary business, and under the laws of that jurisdiction excluding its conflict-of-law provisions. The application of the United Nations Convention on Contracts for the International Sale of Goods is expressly excluded. Any use of the Original Work outside the scope of this License or after its termination shall be subject to the requirements and penalties of the U.S. Copyright Act, 17 U.S.C. § 101 et seq., the equivalent laws of other countries, and international treaty. This section shall survive the termination of this License.
+
+12) Attorneys Fees. In any action to enforce the terms of this License or
+seeking damages relating thereto, the prevailing party shall be entitled
+to recover its costs and expenses, including, without limitation,
+reasonable attorneys' fees and costs incurred in connection with such
+action, including any appeal of such action. This section shall survive
+the termination of this License.
+
+13) Miscellaneous. This License represents the complete agreement
+concerning the subject matter hereof. If any provision of this License
+is held to be unenforceable, such provision shall be reformed only to
+the extent necessary to make it enforceable.
+
+14) Definition of "You" in This License. "You" throughout this License,
+whether in upper or lower case, means an individual or a legal entity
+exercising rights under, and complying with all of the terms of, this
+License. For legal entities, "You" includes any entity that controls,
+is controlled by, or is under common control with you. For purposes of
+this definition, "control" means (i) the power, direct or indirect, to
+cause the direction or management of such entity, whether by contract
+or otherwise, or (ii) ownership of fifty percent (50%) or more of the
+outstanding shares, or (iii) beneficial ownership of such entity.
+
+15) Right to Use. You may use the Original Work in all ways not otherwise
+restricted or conditioned by this License or by law, and Licensor promises
+not to interfere with or be responsible for such uses by You.
+
+This license is Copyright (C) 2003-2004 Lawrence E. Rosen. All rights
+reserved. Permission is hereby granted to copy and distribute this
+license without modification. This license may not be modified without
+the express written permission of its copyright owner.
+
diff --git a/licenses/aldor-2 b/licenses/aldor-2
new file mode 100644
index 000000000..6a2fb288b
--- /dev/null
+++ b/licenses/aldor-2
@@ -0,0 +1,49 @@
+Aldor Public License 2.0
+
+Copyright (C) 1990-2007, Aldor Sofware Organization Ltd
+
+This Aldor distribution contains software and documentation, some in source
+form only, other in source and binary form. Redistribution and use in source
+and binary forms, with or without modification, are permitted provided
+that the following conditions are met:
+
+* Redistributions of source code must retain the original copyright notice,
+ this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the original copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+* Neither the name of the Aldor Software Organization, Aldor.org
+ nor the names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+* If you distribute a modified form of either source or binary code
+ (a) you must make the source form of these modification available to the
+ Aldor Software Organization
+ (b) you grant the Aldor Software Organization a royalty-free license to use,
+ modify or redistribute your modifications without limitation, and
+ (c) you represent that you are legally entitled to grant these rights
+ and that you are not providing the Aldor Software Organization with
+ any code that violates any law or breaches any contract.
+
+* Your redistribution and use is on a non-commercial basis, meaning that no
+ payment is made in connection with it, whether directly (as in payment
+ for a copy of the software) or indirectly (as in payment for some
+ service related to the software, or payment for some product or
+ service that includes a copy of the software "without charge").
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
diff --git a/licenses/blat b/licenses/blat
new file mode 100644
index 000000000..1930d023c
--- /dev/null
+++ b/licenses/blat
@@ -0,0 +1,9 @@
+CONTENTS AND COPYRIGHT
+
+This archive contains the entire source tree for Jim Kent's suite
+of biological analysis and web display programs. All files are
+copyrighted, but license is hereby granted for personal,
+academic, and non-profit use. A license is also granted
+for the contents of the top level lib directory for commercial
+users. Commercial users should contact jim_kent@pacbell.net for
+access to other modules.
diff --git a/licenses/finchtv b/licenses/finchtv
new file mode 100644
index 000000000..ccdf78e48
--- /dev/null
+++ b/licenses/finchtv
@@ -0,0 +1,12 @@
+License Agreement
+
+
+License Grant. Subject to the terms and conditions of this agreement, Geospiza grants the user "the Customer" a perpetual, nontransferable, nonexclusive license to use FinchTV "the Software". The Customer may not sell unauthorized copies of the Software without Geospiza's permission. This agreement does not obligate Geospiza to provide the Customer with updates or enhancements to the Software or future versions of the Software.
+
+Title. Geospiza retains ownership of all of Geospiza's existing copyright, trade secret, patent, trademark, and any other proprietary rights (collectively "Geospiza intellectual property rights") in and to the Software, including all modifications or improvements. Customer acknowledges that it receives only a license to use the Server and Software under this agreement.
+
+Additional Restrictions. Customer will not modify or change the Software without Geospiza's prior written consent. Customer will not decompile, disassemble, or otherwise reverse engineer the Software. Customer agrees that it will not use, disclose, or otherwise communicate any information with respect to the Software that might reasonably be expected to enable copying of all or any portions of the Software. Customer agrees to take reasonable actions to prevent the disclosure to third parties of any information identified by Geospiza as Geospiza confidential or proprietary information.
+
+Warranties, Limitation of Liability, and Indemnification. The Software will be delivered to the Customer "as is." GEOSPIZA MAKES NO WARRANTIES, EXPRESSED OR IMPLIED, INCLUDING WARRANTIES AS TO MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Geospiza will not be liable for special, punitive, indirect, incidental or consequential damages under this agreement whether arising from contract or negligence. In no event will Geospiza's liability to Customer under any claim exceed the total amount paid to Geospiza by Customer under this agreement. No claim or action relating to this agreement may be instituted more than two (2) years after the event giving rise to such action or claim.
+
+General Provisions. Washington state law will govern this agreement. A determination that any provision of this Agreement is invalid, illegal, or unenforceable will not affect the enforceability of any other provision. Neither party will be deemed an agent of the other party for any purpose and the relationship between the parties will only be that of independent contractors. Customer agrees that it will comply with all applicable United States export regulations. Customer further acknowledges that portions of the Software may have been developed using funding from the United States Government. This Agreement is subject to the limited rights granted to the Government in the funding agreement. Any Software supplied directly to the United States Government is classified as "restricted computer software" as defined by section 52.227-19 of the FAR and section 252.227-7013 of the DFARS. All notices and other communications required under this agreement will be in writing and deemed to have been received when personally delivered or when deposited in the United States mail sent registered mail by first-class postage prepaid, addressed as set forth at the beginning of this agreement.
diff --git a/licenses/gmap b/licenses/gmap
new file mode 100644
index 000000000..552d318b4
--- /dev/null
+++ b/licenses/gmap
@@ -0,0 +1,36 @@
+Copyright (c) 2005 Genentech, Inc. All rights reserved.
+
+The Developers of this software are Thomas D. Wu <twu@gene.com> and
+Colin K. Watanabe <ckw@gene.com>.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Package"), to use, copy, and distribute copies of the Package,
+without modifications, provided that the above copyright notice and
+this permission notice are included in all copies or substantial
+portions of the Package. Distribution of this Package as part of a
+commercial software product requires prior arrangement with the
+Developers.
+
+Permission is also hereby granted, free of charge, to any person
+obtaining a copy of this Package, to modify your copy or copies of the
+Package or any portion of it, provided that you use the modified
+Package only within your corporation or organization. Distribution of
+a modified version of this Package requires prior arrangement with the
+Developers.
+
+Genome databases, map files, and other result files produced as output
+from software in this Package do not automatically fall under the
+copyright of this Package, but belong to whoever generated them, and
+may be distributed freely.
+
+IN NO EVENT SHALL GENENTECH, INC. BE LIABLE TO ANY PARTY FOR DIRECT,
+INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, OR OTHER
+LIABILITY, INCLUDING LOST PROFITS, ARISING FROM THE USE OF THIS
+SOFTWARE.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+GENENTECH, INC. HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
+UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
diff --git a/licenses/phrap b/licenses/phrap
new file mode 100644
index 000000000..0e1df110a
--- /dev/null
+++ b/licenses/phrap
@@ -0,0 +1,210 @@
+ACADEMIC USER AGREEMENT
+
+Please read the entire agreement, fill in the information in the
+indicated positions (such as "NAME:"), and return the entire document
+to the indicated people. Please send the document as the message--not
+as an attachment.
+
+Phrap: A program for assembling DNA sequence data.
+
+Swat: A program for searching one or more DNA or protein query sequences
+against a sequence database, using (an efficient implementation of) the
+Smith-Waterman-Gotoh algorithm.
+
+Cross_Match: A general-purpose utility based on Swat for comparing any
+two sets of (long or short) DNA sequences.
+
+Phred: A program that reads DNA sequencer trace data, calls bases,
+assigns quality values to the bases, and writes the base calls and quality
+values to output files.
+
+Consed: A program for viewing and editing Phrap assemblies.
+
+To receive any of these programs you will need to agree to the following
+conditions. They should be taken seriously!
+
+1) You agree to read the documentation. We welcome feedback on any
+inaccuracies.
+
+2) You agree to report any bugs to us. (To fix bugs, we will need
+from you a dataset and a procedure that reproduces the problem; but do
+not send datasets without first emailing us to describe the nature of
+the bug.)
+
+3) You agree not to make the programs (including source code,
+executables, or any part thereof, in modified or unmodified form)
+available to anyone outside your group, and not to put them where they
+may be accessible to outside individuals without your direct knowledge
+(e.g. on a computer to which people outside your group have login
+privileges). The documentation however may be freely distributed.
+Refer any requests for the programs to the authors. If you are
+operating a computer facility which provides access to several
+independent investigators, you agree to set the permissions on the
+executables and source code to allow execute but not read access, so
+that the programs may not be copied. Investigators who want copies of
+the software for their own use must return a separate copy of this
+agreement.
+
+4) You agree not to use the programs for any commercial purpose,
+including but not limited to commercially restricted sequencing
+(defined as sequencing for which a company retains patenting or
+licensing rights regarding the sequence, or the right to restrict or
+delay dissemination of the sequence; with the sole exception that
+sequencing is not considered to be commercially restricted if it is
+federally funded and the investigators adopt the data release policies
+endorsed at the Wellcome Trust-sponsored Bermuda meeting,
+i.e. immediate release of data as it is generated).
+ [If you wish to obtain the software for commercially restricted
+sequencing or any other commercial purposes, you will need to execute
+a separate licensing agreement with the University of Washington and
+pay a fee. In that case please contact:
+
+Lisa Heinz
+University of Washington TechTransfer, Digital Ventures
+Box 354990
+4311-11th Avenue NE, Suite 500
+Seattle, WA 98105-4608
+
+http://depts.washington.edu/techtran
+
+206-616-3451 FAX: 206-616-3322
+swxfr@u.washington.edu
+
+Do not contact her if the academic license applies.]
+
+5) You acknowledge that the software is experimental in nature and is
+supplied "AS IS", without obligation by the authors or the University
+of Washington to provide accompanying services or support. The entire
+risk as to the quality and performance of the Software is with you.
+UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES
+REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT
+LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A
+PARTICULAR PURPOSE.
+
+6) All members of your group with access to the software agree to the
+same conditions.
+
+
+
+Having read the above, if you are still interested in obtaining the
+programs, please return a copy of this entire message (which MUST be
+included so that it is clear what you are agreeing to) by email
+together with the following information:
+
+NAME: Your name in first name/last name order.
+
+NAME:
+
+
+Example:
+NAME: John Dracula
+(Please do not use all capitals such as John DRACULA)
+
+ACKNOWLEDGEMENT: An acknowledgement that you and the members of your
+group agree to these conditions.
+
+ACKNOWLEDGEMENT:
+
+Example:
+ACKNOWLEDGEMENT: I agree to the license.
+
+PROGRAMS: Which programs you want (phrap,cross_match, and swat are
+distributed together). You must cc the message to each appropriate
+individual (Brent Ewing, David Gordon, and/or Phil Green) at the email
+addresses below so that they will know to send you the appropriate
+program.
+
+PROGRAMS:
+
+Example:
+PROGRAMS: phred, phrap, consed
+
+INSTITUTION: Your academic or government institution (give full name,
+not abbreviation)
+
+INSTITUTION:
+
+Example:
+INSTITUTION: University of Lower Transylvania
+
+DEPARTMENT: Your department
+
+DEPARTMENT:
+
+Example:
+DEPARTMENT: Department of Hematology
+
+EMAIL: Your email address for all future correspondence. Ideally this
+should be a Unix computer running a generic mail program, since
+several of the programs are sent as uuencoded files which may be
+corrupted by some mail programs.
+ If this address is not at the institution & department listed above,
+please explain the discrepancy.
+
+EMAIL:
+
+Example:
+EMAIL: john.dracula@utrans.edu
+
+OS: (Consed requestors only) Which platform(s) you want Consed for:
+solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8,
+solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2,
+6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better),
+linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2
+(Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better).
+
+OS:
+
+Example:
+OS: hpux
+
+Note: Consed is not available for PC's running Windows, XP, NT, or
+2000.
+
+IP: (Consed requestors only) The ip address of the computer on which
+you will be running a web browser to download consed. This does not
+have to be the same computer as the one on which you will run consed.
+Please view page
+http://bozeman.mbt.washington.edu/consed/find_ip_address.html
+which will tell you what my computer thinks is your ip address.
+
+(Even if you think you know your ip address, firewalls and proxies can
+cause your browser to transmit a different ip address, and thus my
+webserver would deny you access to consed. So it would be a good idea
+to view the page above and send me the ip address it shows, even if
+this isn't your real ip address.)
+
+IP:
+
+Example:
+IP: 123.49.74.80
+
+
+If you want Consed/Autofinish, you must include OS and IP (above).
+Consed cannot be obtained without them.
+
+Please return this entire agreement so it is clear what you are
+agreeing to.
+
+Please send all of this, including the agreement, as part of the
+email message--not as an attachment.
+
+Send it to each of the relevant individuals below:
+
+Contacts for obtaining the programs and for questions, bug reports,
+suggestions:
+
+ Phrap/cross_match/swat: Phil Green, phg (at) u.washington.edu
+ Phred: Brent Ewing, bge (at) u.washington.edu
+ Consed: David Gordon, gordon (at) genome.washington.edu
+
+where the " (at) " is replaced by "@".
+
+It can take up to 2 weeks for a license application to be processed,
+so please be patient.
+
+
+
+
+
+
diff --git a/net-ftp/bbftp-client/ChangeLog b/net-ftp/bbftp-client/ChangeLog
new file mode 100644
index 000000000..de82fc25d
--- /dev/null
+++ b/net-ftp/bbftp-client/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for net-ftp/bbftp-client
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bbftp-client-3.2.0 (01 Dec 2007)
+
+ 01 Dec 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ initial import
+
diff --git a/net-ftp/bbftp-client/Manifest b/net-ftp/bbftp-client/Manifest
new file mode 100644
index 000000000..8a6eec8aa
--- /dev/null
+++ b/net-ftp/bbftp-client/Manifest
@@ -0,0 +1,4 @@
+DIST bbftp-client-3.2.0.tar.gz 233948 RMD160 9c11f6734bfa66667bb3aa690dbb3e661779e8b0 SHA1 90900c672f8b68b6b0bade3b6f66931722b6a2ae SHA256 b533de28f517671adad177532b6f4ae66c30e4ce3d2f558d1d7e6b172d96bcb6
+EBUILD bbftp-client-3.2.0.ebuild 969 RMD160 71c34d6befc2d48d4e39cd03e191338b1c6ad653 SHA1 1cafaf339118a290d625c12d6d06e9d45024c884 SHA256 6a72dcf2687feb0008ea79e3bfe44244ef6fe064844753f0c86a52232a5ce469
+MISC ChangeLog 237 RMD160 e92c4f780d9539719a1c33e474c6ab372b261b66 SHA1 a5c04d39ab4e4ec6f25584e8c6e0a89cd8dcad33 SHA256 910b6190a97294ba7f678f736249069b0881c7f8a7fedf02c11d5e780e02093f
+MISC metadata.xml 417 RMD160 cee5a58bdcc8778dc746f29717bad69c6d6de8a3 SHA1 d846f619290fff9989b195e6f3a4a6b381b0a7d2 SHA256 7bd69c2ffa53bba43140b5019c71d571bc024d5abb1f9a3e5b638296333324df
diff --git a/net-ftp/bbftp-client/bbftp-client-3.2.0.ebuild b/net-ftp/bbftp-client/bbftp-client-3.2.0.ebuild
new file mode 100644
index 000000000..0f59a9336
--- /dev/null
+++ b/net-ftp/bbftp-client/bbftp-client-3.2.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information."
+
+HOMEPAGE="http://doc.in2p3.fr/bbftp/"
+SRC_URI="http://doc.in2p3.fr/bbftp/dist/${P}.tar.gz"
+S="${WORKDIR}/${P}/bbftpc"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="ssl"
+
+DEPEND="ssl? ( dev-libs/openssl )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ sed -i -e '/@INSTALL@\|mkdir/s:${\(prefix\|mandir\|bindir\)}:${DESTDIR}${\1}:' -e '/\/etc/d' Makefile.in
+ econf $(use_with ssl) --with-gzip \
+ --without-rfio \
+ --without-afs || die "configure failed"
+ emake
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ dodoc ../README ../ChangeLog ../TODO
+ dodoc ../doc/*
+ doman ../doc/bbftp.1
+}
+
diff --git a/net-ftp/bbftp-client/metadata.xml b/net-ftp/bbftp-client/metadata.xml
new file mode 100644
index 000000000..7e915aa7e
--- /dev/null
+++ b/net-ftp/bbftp-client/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription>
+bbFTP is a file transfer software. It implements its own transfer protocol,
+which is optimized for large files (larger than 2GB) and secure as it does not
+read the password in a file and encrypts the connection information.
+</longdescription>
+</pkgmetadata>
diff --git a/net-ftp/bbftp-server/ChangeLog b/net-ftp/bbftp-server/ChangeLog
new file mode 100644
index 000000000..b6badb800
--- /dev/null
+++ b/net-ftp/bbftp-server/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for net-ftp/bbftp-server
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bbftp-server-3.2.0 (01 Dec 2007)
+
+ 01 Dec 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ initial import
+
diff --git a/net-ftp/bbftp-server/Manifest b/net-ftp/bbftp-server/Manifest
new file mode 100644
index 000000000..b0e27ab08
--- /dev/null
+++ b/net-ftp/bbftp-server/Manifest
@@ -0,0 +1,5 @@
+AUX bbftpd.init.d 698 RMD160 dc9f9976ff02e2de1e7c37eb0f2ffc21fc4ad65a SHA1 9793f3d17555508b0aa08b2e1e2b986f46b6ca5e SHA256 e7b81c6034f8298ea2fd232338c1f309d3554a76f1dff8d8c1658eefcebe5163
+DIST bbftp-server-3.2.0.tar.gz 222600 RMD160 a6c8a79f8bf06dc7674331168a9bf705029edd12 SHA1 dc599051ed69093caaed029e1a0c28614f7f080d SHA256 04fbe472dc4c39f5b3e82520c08a084e8c4fd5301242c6bbb934d6984013b8ff
+EBUILD bbftp-server-3.2.0.ebuild 1207 RMD160 66e58a948d0043f4bd2655087963afe11f4f94f7 SHA1 c3cacb82c10482fc67afc3284e86f27c266bd47d SHA256 402d51a00f1591f04a50076708eaaabcb15cf69f26686f7e6a84f4db06bd542b
+MISC ChangeLog 237 RMD160 6756877e22081514c09ffc5b4b97e58e047fdd5c SHA1 6ffcaefa9ad726189b22c848ee49f829cb339090 SHA256 c6e43425f23863c6cbe59efce2e62c5625b7259fdaa87c8a6417d04d8d52802f
+MISC metadata.xml 417 RMD160 cee5a58bdcc8778dc746f29717bad69c6d6de8a3 SHA1 d846f619290fff9989b195e6f3a4a6b381b0a7d2 SHA256 7bd69c2ffa53bba43140b5019c71d571bc024d5abb1f9a3e5b638296333324df
diff --git a/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild b/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild
new file mode 100644
index 000000000..48aa0b3e0
--- /dev/null
+++ b/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information."
+
+HOMEPAGE="http://doc.in2p3.fr/bbftp/"
+SRC_URI="http://doc.in2p3.fr/bbftp/dist/${P}.tar.gz"
+S="${WORKDIR}/${P}/bbftpd"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="ssl pam"
+
+DEPEND="ssl? ( dev-libs/openssl )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ sed -i -e '/@INSTALL@\|mkdir/s:${\(prefix\|mandir\|bindir\)}:${DESTDIR}${\1}:' -e '/\/etc/d' Makefile.in
+ econf $(use_with ssl) $(use_with pam) --with-gzip \
+ --without-rfio \
+ --without-afs || die "configure failed"
+ emake
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+ newinitd "${FILESDIR}/bbftpd.init.d" bbftpd
+ dodoc ../README ../ChangeLog ../TODO
+ dodoc ../doc/*
+ doman ../doc/bbftpd.1
+ if use pam; then
+ echo -e "#%PAM-1.0\nauth include system-auth\naccount include system-auth" >> "${T}/bbftp.pam"
+ insinto /etc/pam.d
+ newins "${T}/bbftp.pam" bbftp
+ fi
+}
+
diff --git a/net-ftp/bbftp-server/files/bbftpd.init.d b/net-ftp/bbftp-server/files/bbftpd.init.d
new file mode 100755
index 000000000..65da2d5b6
--- /dev/null
+++ b/net-ftp/bbftp-server/files/bbftpd.init.d
@@ -0,0 +1,28 @@
+#!/sbin/runscript
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# Based on opensm script from openfabrics.org,
+# Copyright (c) 2006 Mellanox Technologies. All rights reserved.
+# Distributed under the terms of the GNU General Public License v2
+
+depend() {
+ after net # ip net seems to be needed to perform management.
+}
+
+prog=/usr/bin/bbftpd
+pidfile=/var/run/bbftpd.pid
+
+start() {
+ ebegin "Starting bbftpd"
+ start-stop-daemon --start --pidfile $pidfile --exec $prog -- -b $OPTIONS
+ eend $?
+}
+
+stop() {
+ ebegin "Stopping bbftpd"
+ start-stop-daemon --stop --pidfile $pidfile --exec $prog
+ eend $?
+}
+
diff --git a/net-ftp/bbftp-server/metadata.xml b/net-ftp/bbftp-server/metadata.xml
new file mode 100644
index 000000000..7e915aa7e
--- /dev/null
+++ b/net-ftp/bbftp-server/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription>
+bbFTP is a file transfer software. It implements its own transfer protocol,
+which is optimized for large files (larger than 2GB) and secure as it does not
+read the password in a file and encrypts the connection information.
+</longdescription>
+</pkgmetadata>
diff --git a/net-misc/bbscp/ChangeLog b/net-misc/bbscp/ChangeLog
new file mode 100644
index 000000000..595c97f87
--- /dev/null
+++ b/net-misc/bbscp/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for net-misc/bbscp
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bbscp-1.0.4 (04 Dec 2007)
+
+ 04 Dec 2007; Bryan Green <bryan.d.green@nasa.gov> ChangeLog:
+ initial import
+
diff --git a/net-misc/bbscp/Manifest b/net-misc/bbscp/Manifest
new file mode 100644
index 000000000..4ed8f222a
--- /dev/null
+++ b/net-misc/bbscp/Manifest
@@ -0,0 +1,4 @@
+DIST bbscp-1.0.4.tar.gz 17411 RMD160 23f309b99e5fddecc5d82e7dc7db38c9f5f4187d SHA1 419cf864f6c3f54ec6a393be478ceb3a8198b77f SHA256 c3abb35f905d90b4db75be11cbbcd4fa9b89d674bc1430d5fbe8e71557ca9642
+EBUILD bbscp-1.0.4.ebuild 546 RMD160 3c34ff463ea9fbda0269b39cc5c1bd31b658fcd7 SHA1 a890ccb0f778f02c49b6309f801d3c6889281754 SHA256 dae5b9b7933aaec32bc6d1402b095d841428a0cbaa246491eb0d6ac4ebccd67a
+MISC ChangeLog 224 RMD160 64ad110995913b1f7aa6698fcbb3248f132c8db4 SHA1 cbbcbbb8c26cb70adc042c9042d66051c420bbaa SHA256 ed5ae860ea72c0f8761aefd62d934b598af176bd56549c146efe5ab353cb90c3
+MISC metadata.xml 258 RMD160 d978601c9331b847f432d1bc19ba06d676ef8f85 SHA1 8866f844d2e77b330bc45748953d4c8619cdd065 SHA256 21ddbacc6fbe6168ee7a3a1f97bc535c99e6dee91aaf7f8581ca6a603b9387a1
diff --git a/net-misc/bbscp/bbscp-1.0.4.ebuild b/net-misc/bbscp/bbscp-1.0.4.ebuild
new file mode 100644
index 000000000..35edcfd99
--- /dev/null
+++ b/net-misc/bbscp/bbscp-1.0.4.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="bbSCP is a wrapper that provides an SCP-like interface to bbFTP."
+
+HOMEPAGE="http://www.nas.nasa.gov/Users/Documentation/Networks/BBSCP/bbscp.html"
+SRC_URI="http://www.nas.nasa.gov/Users/Documentation/Networks/BBSCP/${P}.tar.gz"
+
+LICENSE="NOSA"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND} net-ftp/bbftp-client"
+
+src_install() {
+ dobin bbscp
+ dodoc NOSA.txt COPYING.txt
+ doman man/bbscp.1
+}
+
diff --git a/net-misc/bbscp/metadata.xml b/net-misc/bbscp/metadata.xml
new file mode 100644
index 000000000..aacb31534
--- /dev/null
+++ b/net-misc/bbscp/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription>
+bbSCP is a wrapper that provides an SCP-like interface to bbFTP.
+</longdescription>
+</pkgmetadata>
diff --git a/profiles/categories b/profiles/categories
new file mode 100755
index 000000000..d9e6bb317
--- /dev/null
+++ b/profiles/categories
@@ -0,0 +1,18 @@
+app-office
+dev-cpp
+dev-lang
+dev-python
+dev-tcltk
+dev-util
+media-libs
+sci-astronomy
+sci-biology
+sci-chemistry
+sci-electronics
+sci-libs
+sci-mathematics
+sci-misc
+sci-physics
+sci-visualization
+sys-cluster
+x11-libs
diff --git a/profiles/repo_name b/profiles/repo_name
new file mode 100755
index 000000000..8ebbbd48b
--- /dev/null
+++ b/profiles/repo_name
@@ -0,0 +1 @@
+science
diff --git a/profiles/use.local.desc b/profiles/use.local.desc
new file mode 100644
index 000000000..823f8aeaf
--- /dev/null
+++ b/profiles/use.local.desc
@@ -0,0 +1,49 @@
+# Copyright 1999-2006 Gentoo Foundation.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# This file contains descriptions of local USE flags, and the ebuilds which
+# contain them.
+# Keep it sorted.
+
+# We keep here only the new USE flags introduced by packages in the overlay.
+# Ultimately, they will be merged into the main tree.
+
+app-office/texmacs:netpbm - Allows TeXmacs to include images in a number of formats
+sci-astronomy/scamp:plplot - Add plplot to allow diagnostic plots during processing
+sci-biology/tgi-tools:pvm - Use sys-cluster/pvm (Parallel Virtual Machine) and build the pvmsx utility
+sci-mathematics/gap:xtom - extra tables of marks
+sci-mathematics/netgen:opencascade - Enable OpenCASCADE support
+sci-misc/opencascade/opencascade:draw-harness - Enable building of draw-harness
+sci-misc/opencascade/opencascade:stlport - Build OpenCASCADE with STLPort
+sci-misc/opencascade/opencascade:wok - Enable building of WOK
+sci-misc/opennlp-tools:models - Install prebuild ME models (requires a ton of disk space)
+sci-physics/clhep:exceptions - Build CLHEP with exception mechanism
+sci-physics/meep:hdf5 - Enable support for the Hierarchical Data Format version 5
+sci-visualization/nodemon:pbs - Adds support for PBS (Portable Batch System) queries
+sci-visualization/fityk:gnuplot - Add gnuplot support, useful for command line
+sys-cluster/openib:dapl - add DAPL (Direct Access Provider Library) support.
+sys-cluster/openib:ipath - add PathScale HCA support.
+sys-cluster/openib:opensm - add OpenSM Subnet Management support.
+sys-cluster/openib-drivers:memtrack - enable momory tracking
+sys-cluster/openib-drivers:hpage-patch - apply huge pages patch
+sys-cluster/openib-drivers:srp - make CONFIG_INFINIBAND_SDP=m
+sys-cluster/openib-drivers:ipath - make CONFIG_INFINIBAND_IPATH=m
+sys-cluster/openib-drivers:iser - make CONFIG_INFINIBAND_ISER=m
+sys-cluster/openib-drivers:ehca - make CONFIG_INFINIBAND_EHCA=m
+sys-cluster/openib-drivers:rds - make CONFIG_RDS=m
+sys-cluster/openib-drivers:madeye - make CONFIG_INFINIBAND_MADEYE=m
+sys-cluster/openib-drivers:vnic - make CONFIG_INFINIBAND_VNIC=m
+sys-cluster/openib-drivers:cxgb3 - make CONFIG_INFINIBAND_CXGB3=m
+sys-cluster/openib-userspace:srptools - include srptools package
+sys-cluster/openib-userspace:ehca - include libehca package
+sys-cluster/openib-userspace:ipath - add PathScale HCA support
+sys-cluster/openib-userspace:cxgb3 - include libcxgb3 package
+sys-cluster/openib-userspace:opensm - add OpenSM Subnet Management support.
+sys-cluster/openib-userspace:dapl - add DAPL (Direct Access Provider Library) support
+sys-cluster/openib-userspace:qlvnictools - include qlvnictools package
+sys-cluster/openib-userspace:tvflash - include tvflash package
+sys-cluster/openib-userspace:mstflint - include mstflint package
+sys-cluster/openib-mvapich2:large-cluster - build _LARGE_CLUSTER configuration
+sys-cluster/openib-mvapich2:medium-cluster - build _MEDIUM_CLUSTER configuration
+sys-cluster/openib-mvapich2:rdma - use rdmacm
diff --git a/sci-astronomy/cdsclient/ChangeLog b/sci-astronomy/cdsclient/ChangeLog
new file mode 100644
index 000000000..3032d8a7f
--- /dev/null
+++ b/sci-astronomy/cdsclient/ChangeLog
@@ -0,0 +1,21 @@
+# ChangeLog for sci-astronomy/cdsclient
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cdsclient-2.89 (07 Nov 2007)
+
+ 07 Nov 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ -cdsclient-2.87.ebuild, +cdsclient-2.89.ebuild:
+ Version bump
+
+*cdsclient-2.87 (26 Mar 2007)
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ +cdsclient-2.87.ebuild:
+ Version bump.
+
+*cdsclient-2.85 (19 Sep 2006)
+
+ 19 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> cdsclient-2.85.ebuild
+ Initial import.
+
diff --git a/sci-astronomy/cdsclient/Manifest b/sci-astronomy/cdsclient/Manifest
new file mode 100644
index 000000000..a2c7cacf5
--- /dev/null
+++ b/sci-astronomy/cdsclient/Manifest
@@ -0,0 +1,4 @@
+DIST cdsclient-2.89.tar.gz 77883 RMD160 4b93a4fb184b0b25d5aa61f64495fe828a2d40a3 SHA1 741ac0ef16570db04d1659cd0bbf685633ca1f37 SHA256 55695e67b79808b5422682d9094ff67ce12a6384e4feb4de42e7e55e74391677
+EBUILD cdsclient-2.89.ebuild 1016 RMD160 e8906b24707e470c9b891a1aa3c20c54db2a51c4 SHA1 f495d1b11beba296493cc26eb95640db64f4c6c3 SHA256 c04c45c5e57742bebd26554e87d0461c3ca62bd35b8330f9f6089a73a58d2122
+MISC ChangeLog 533 RMD160 ea4f6c529882cd00266e7e047e0ee5ff699d6d60 SHA1 8e459d4845b2c7ff9edaae660e8d4665711eee3b SHA256 e06398c9a5eeca00458db543a30f2d881253dde717f248b76402bb715748f028
+MISC metadata.xml 420 RMD160 110bdf15554e88e236e4a9e40ba8a3470d696c96 SHA1 a7a8719fb8473e02ae8b70f88bd51a147c6da202 SHA256 343e595f7f12b920acd268121fa2c429d269a6e2c2690d4c917ea4855c7c687c
diff --git a/sci-astronomy/cdsclient/cdsclient-2.89.ebuild b/sci-astronomy/cdsclient/cdsclient-2.89.ebuild
new file mode 100644
index 000000000..c279e4808
--- /dev/null
+++ b/sci-astronomy/cdsclient/cdsclient-2.89.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit multilib
+
+DESCRIPTION="Collection of scripts to access the CDS databases"
+HOMEPAGE="http://cdsweb.u-strasbg.fr/doc/cdsclient.html"
+SRC_URI="ftp://cdsarc.u-strasbg.fr/pub/sw/${P}.tar.gz"
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+RESTRICT="strip"
+
+src_unpack() {
+ unpack ${A}
+ # remove non standard "mantex" page
+ sed -i \
+ -e 's/aclient.tex//' \
+ "${S}"/configure || die "sed failed"
+ # remove useless version file
+ sed -i \
+ -e 's/install_shs install_info/install_shs/' \
+ "${S}"/Makefile.in || die "sed failed"
+}
+
+src_compile() {
+ econf || die "econf failed"
+ emake C_OPT="${CFLAGS}" || die "emake failed"
+}
+
+
+src_install() {
+ dodir /usr/bin
+ dodir /usr/share/man
+ dodir /usr/$(get_libdir)
+ emake \
+ PREFIX="${D}"/usr \
+ MANDIR="${D}"/usr/share/man \
+ LIBDIR="${D}"/usr/$(get_libdir) \
+ install || die "emake install failed"
+}
diff --git a/sci-astronomy/cdsclient/metadata.xml b/sci-astronomy/cdsclient/metadata.xml
new file mode 100644
index 000000000..7d603f33d
--- /dev/null
+++ b/sci-astronomy/cdsclient/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ The cdsclient package is a set of C and csh routines which can be
+ built on Unix stations or PCs running Linux, which once compiled allow
+ to query some databases located at CDS or on mirrors over the
+ network.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/cpl/ChangeLog b/sci-astronomy/cpl/ChangeLog
new file mode 100644
index 000000000..3fc3f612c
--- /dev/null
+++ b/sci-astronomy/cpl/ChangeLog
@@ -0,0 +1,14 @@
+# ChangeLog for sci-astronomy/cpl
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org> -cpl-3.0.ebuild,
+ +cpl-3.1.ebuild:
+ Version bump.
+
+*cpl-3.0 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ +cpl-3.0.ebuild, +metadata.xml.
+ Initial import.
+ \ No newline at end of file
diff --git a/sci-astronomy/cpl/Manifest b/sci-astronomy/cpl/Manifest
new file mode 100644
index 000000000..f46376b1d
--- /dev/null
+++ b/sci-astronomy/cpl/Manifest
@@ -0,0 +1,4 @@
+DIST cpl-3.1.tar.gz 1971557 RMD160 70fd7a764743203c740bbf43e878292feab879ff SHA1 e564d89ee3018f81d75da44c4f861b6aef93c1cb SHA256 d98a51f4606c677151b57b8b2576803a8e18b145b74921ef3948f60206ec8085
+EBUILD cpl-3.1.ebuild 618 RMD160 89499f7d55620078c249b95794b34aa8dd28dd25 SHA1 33f60f8a82ac6e664ff4592ad35efc5d088d133b SHA256 7c86df593f9053b4530a92b4dfee92c75f039d8f30f51c5b65c45e3200f2a436
+MISC ChangeLog 355 RMD160 11ab72f28cd1b842e0a933e43a937d4241f7bb41 SHA1 49eea80ef4e138306853e879dfef6adb56be3afb SHA256 7132771ff2f54997da312e48808bcef6d9afdc8c611008c6d7c4bbe5bf02873d
+MISC metadata.xml 831 RMD160 954a38f6449d8d3e9ff0c63abb55154768adc088 SHA1 97a67157b2448b61ba012e89b60ef73108235873 SHA256 7d1222b0691f211f2030e22c5481f3a6cb01e95486f904030dc1f2136b446149
diff --git a/sci-astronomy/cpl/cpl-3.1.ebuild b/sci-astronomy/cpl/cpl-3.1.ebuild
new file mode 100644
index 000000000..645e9cf50
--- /dev/null
+++ b/sci-astronomy/cpl/cpl-3.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="ESO common pipeline library for astronomical data reduction"
+HOMEPAGE="http://www.eso.org/observing/cpl/"
+SRC_URI="ftp://ftp.hq.eso.org/pub/${PN}/${P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=">=sci-libs/qfits-6.2"
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc README AUTHORS NEWS TODO BUGS ChangeLog
+ if use doc; then
+ make htmldir=usr/share/doc/${PF} install-html \
+ || die "make install-html failed"
+ fi
+}
diff --git a/sci-astronomy/cpl/metadata.xml b/sci-astronomy/cpl/metadata.xml
new file mode 100644
index 000000000..2a13944f0
--- /dev/null
+++ b/sci-astronomy/cpl/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+The Common Pipeline Library (CPL) comprises a set of ISO-C libraries
+that provide a comprehensive, efficient and robust software
+toolkit. It forms a basis for the creation of automated astronomical
+data-reduction tasks (known as "pipelines"). CPL Title Graphic The CPL
+was developed to standardise the way VLT instrument pipelines are
+built, to shorten their development cycle and to ease their
+maintenance. However, it may be more generally applied to any similar
+application, and the details of the CPL code have been engineered in a
+way to make the library portable and flexible, as well as minimising
+external dependencies.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/esorex/ChangeLog b/sci-astronomy/esorex/ChangeLog
new file mode 100644
index 000000000..04a23467a
--- /dev/null
+++ b/sci-astronomy/esorex/ChangeLog
@@ -0,0 +1,14 @@
+# ChangeLog for sci-astronomy/esorex
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org> -esorex-3.6.ebuild,
+ +esorex-3.6.1.ebuild:
+ Version bump.
+
+*esorex-3.6 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ +esorex-3.6.ebuild, +metadata.xml.
+ Initial import.
+ \ No newline at end of file
diff --git a/sci-astronomy/esorex/Manifest b/sci-astronomy/esorex/Manifest
new file mode 100644
index 000000000..d113c11cc
--- /dev/null
+++ b/sci-astronomy/esorex/Manifest
@@ -0,0 +1,4 @@
+DIST esorex-3.6.1.tar.gz 724825 RMD160 ce94b38c4800e5b88d481db36cac3dbdc6a965d2 SHA1 a07271d4baed4a4b0edd85f7fb172d9a0e234e7d SHA256 cae6b17f7ef9eb66e5898b60bbfcd0fddb1af2d8b79ed0f792bcb3772e7a3216
+EBUILD esorex-3.6.1.ebuild 546 RMD160 68756a5cc917a39d3934189a02e17f129992cb03 SHA1 be98fcb153bee10521527595ba8aabed3fe7b481 SHA256 47a34ea7bd1becfa2e045fce0ae59d26354fcc5c7697d337c000bacbd3409277
+MISC ChangeLog 372 RMD160 fb067a660b1ecd6ecf44e62f23a84bf2076b46cf SHA1 49237b69bf75c3ec132313437579676dee9eac50 SHA256 b55dc336b090b1e53312ef9b5070c9284da533a41be828ce09cc7b380fef7cf4
+MISC metadata.xml 893 RMD160 c1619c4f959c27d9042fcaba4e716ca685d9d831 SHA1 42826c66a8ff7b789648441c617eea57d8688177 SHA256 145c6d216327ba207bf3d19435de54ff30d3a0df8169f34e70c558b97aa62a19
diff --git a/sci-astronomy/esorex/esorex-3.6.1.ebuild b/sci-astronomy/esorex/esorex-3.6.1.ebuild
new file mode 100644
index 000000000..11468a645
--- /dev/null
+++ b/sci-astronomy/esorex/esorex-3.6.1.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="ESO Recipe Execution Tool to exec cpl scripts"
+HOMEPAGE="http://www.eso.org/observing/cpl/esorex"
+SRC_URI="ftp://ftp.hq.eso.org/pub/cpl/${P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+DEPEND=">=sci-astronomy/cpl-3.1"
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc README AUTHORS NEWS TODO BUGS ChangeLog
+ insinto /usr/share/doc/${PF}
+ doins examples/*
+}
diff --git a/sci-astronomy/esorex/metadata.xml b/sci-astronomy/esorex/metadata.xml
new file mode 100644
index 000000000..d65df3197
--- /dev/null
+++ b/sci-astronomy/esorex/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+EsoRex is the ESO Recipe Execution Tool. It can list, configure and
+execute CPL-based recipes from the command line. One of the features
+provided by the CPL is the ability to create data-reduction algorithms
+that run as plugins (dynamic libraries). These are called recipes and
+are one of the main aspects of the CPL data-reduction development
+environment. As these recipes are dynamic libraries, it is not
+possible to run them directly from the command line. However, ESO
+provides several tools to do this, thus saving recipe developers the
+need to write such an application themselves. One of these is GASGANO
+(a GUI-based tool) and the other is EsoRex (which runs from the
+command line.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/scamp/ChangeLog b/sci-astronomy/scamp/ChangeLog
new file mode 100644
index 000000000..e8751e27f
--- /dev/null
+++ b/sci-astronomy/scamp/ChangeLog
@@ -0,0 +1,33 @@
+# ChangeLog for sci-astronomy/scamp
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 08 Nov 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ +files/scamp-atlas.patch, -scamp-1.3.11.ebuild, +scamp-1.4.0.ebuild:
+ Version bump
+
+ 02 Aug 2007; Sébastien Fabbro <bicatali@gentoo.org> -scamp-1.3.8.ebuild,
+ +scamp-1.3.11.ebuild:
+ Version bump
+
+ 18 May 2007; Sébastien Fabbro <bicatali@gentoo.org> -scamp-1.3.5.ebuild,
+ +scamp-1.3.8.ebuild:
+ Version bump
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ -scamp-1.2.11-r1.ebuild, +scamp-1.3.5.ebuild:
+ Version bump.
+
+ 29 Dec 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ Removed icc flag, too buggy.
+
+*scamp-1.2.11-r1 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt> +scamp-1.2.11-r1.ebuild:
+ Removed flag filtering, some cleaning.
+
+*scamp-1.2.11 (19 Sep 2006)
+
+ 19 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> +scamp-1.2.11.ebuild:
+ Initial import.
+
diff --git a/sci-astronomy/scamp/Manifest b/sci-astronomy/scamp/Manifest
new file mode 100644
index 000000000..2e4bde801
--- /dev/null
+++ b/sci-astronomy/scamp/Manifest
@@ -0,0 +1,5 @@
+AUX scamp-atlas.patch 770 RMD160 6e884c055bc97fe1938b8d17fa514014e432ef5a SHA1 df65f3f0e767da037cd673578fabceeeaf9bfc6d SHA256 b3e8e3b8946bfa9304a5ccbacde451591b51cd872025fc7093d3ba71b8733530
+DIST scamp-1.4.0.tar.gz 17723603 RMD160 6de11f8666cb6e3065c49d5064cefa884aa23697 SHA1 d1c8cd64baa359d7cd01d09dbcb8ec0560879ad9 SHA256 c79c9ced15a7dba4788048541518f7d26562e8690dbdc67043f9430f4bc29dc3
+EBUILD scamp-1.4.0.ebuild 1451 RMD160 d5697bac7ca8c69d4100be34eb1cc16b90d845a9 SHA1 5586b3e08eadaa230133116531b651035c1403be SHA256 a9c4e304747644436f43925f4faf59c9a96005af72c7ec85ab928701d8a632e8
+MISC ChangeLog 963 RMD160 a4aaa0ba53721f221c69b5204dd41fd272f80a23 SHA1 27df2261e842eff7915b3c8de20c33f2e87ad28d SHA256 d102da08211ff0778eb8c93df673fe81752dbf5484635e4d4c2ffb77d0710e8b
+MISC metadata.xml 378 RMD160 51f393d1e79301572f09a1c7bce449e14289f9a1 SHA1 0115b4e450192e8eec4a1236eba31e871eecc055 SHA256 9a28c3abd3899bd79ae8aa958492e89a5fb644f2102a714862a8de7e0bcb1706
diff --git a/sci-astronomy/scamp/files/scamp-atlas.patch b/sci-astronomy/scamp/files/scamp-atlas.patch
new file mode 100644
index 000000000..3df2b5bc3
--- /dev/null
+++ b/sci-astronomy/scamp/files/scamp-atlas.patch
@@ -0,0 +1,25 @@
+--- configure.ac.orig 2007-11-08 15:38:10.146227506 +0000
++++ configure.ac 2007-11-08 15:38:35.895694885 +0000
+@@ -217,11 +217,7 @@
+
+ ################## handle the ATLAS library(linear algebra) ##################
+ if test "$use_atlas" = "yes"; then
+- if test "$use_pthreads" = "yes"; then
+- LIBS="-llapack -lptcblas -lcblas -latlas $LIBS"
+- else
+- LIBS="-llapack -lcblas -latlas $LIBS"
+- fi
++ LIBS="ATLAS_LIBDIR -llapack -lcblas -latlas $LIBS"
+ else
+ AC_MSG_ERROR([CBLAS/LAPack library not found! Exiting.])
+ fi
+--- src/Makefile.am.orig 2007-11-08 15:38:45.072217825 +0000
++++ src/Makefile.am 2007-11-08 15:39:24.090441347 +0000
+@@ -4,6 +4,7 @@
+
+ if USE_PLPLOT
+ CPLOTSOURCE = cplot.c
++AM_CFLAGS = @PLPLOT_CFLAGS@ $(CFLAGS)
+ endif
+
+ bin_PROGRAMS = scamp
diff --git a/sci-astronomy/scamp/metadata.xml b/sci-astronomy/scamp/metadata.xml
new file mode 100644
index 000000000..60a0fc95d
--- /dev/null
+++ b/sci-astronomy/scamp/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ SCAMP computes astrometric and photometric solutions from SExtractor catalogs
+ and stores them in header files. These headers files can be read by SWarp to
+ coadd images.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/scamp/scamp-1.4.0.ebuild b/sci-astronomy/scamp/scamp-1.4.0.ebuild
new file mode 100644
index 000000000..067c5ebb5
--- /dev/null
+++ b/sci-astronomy/scamp/scamp-1.4.0.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils autotools
+
+DESCRIPTION="Computes astrometric and photometric solutions for astronomical images"
+HOMEPAGE="http://terapix.iap.fr/soft/scamp"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc threads plplot"
+RESTRICT="test"
+
+DEPEND="sci-astronomy/cdsclient
+ >=sci-libs/lapack-atlas-3.8.0
+ >=sci-libs/fftw-3
+ sci-libs/plplot"
+# plplot option buggy if removed, force it for now.
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ # gentoo specific patch for atlas lib dir and lib names
+ epatch "${FILESDIR}"/${PN}-atlas.patch
+
+ # fix libdir if threaded
+ local myatlas="/usr/$(get_libdir)/blas/atlas"
+ if use threads && \
+ [ -f /usr/$(get_libdir)/blas/threaded-atlas/libcblas.a ]; then
+ myatlas="/usr/$(get_libdir)/blas/threaded-atlas"
+ fi
+ myatlas="-L${myatlas} -L/usr/$(get_libdir)/lapack/atlas"
+ sed -i -e "s:ATLAS_LIBDIR:${myatlas}:" configure.ac || die "configure.ac not found"
+
+ eautoreconf
+}
+
+src_compile() {
+ econf \
+ $(use_enable threads) \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install () {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS || die
+ if use doc; then
+ insinto /usr/share/doc/${PF}
+ doins doc/${PN}.pdf || die "pdf doc install failed"
+ fi
+}
diff --git a/sci-astronomy/sextractor/ChangeLog b/sci-astronomy/sextractor/ChangeLog
new file mode 100644
index 000000000..445f0675b
--- /dev/null
+++ b/sci-astronomy/sextractor/ChangeLog
@@ -0,0 +1,32 @@
+# ChangeLog for sci-astronomy/sextractor
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 02 Aug 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ sextractor-2.5.0-r1.ebuild:
+ filter optim flags
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ sextractor-2.5.0-r1.ebuild:
+ Cleaning, adapting for new portage.
+
+ 29 Dec 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ Removed icc flag, too buggy.
+
+*sextractor-2.5.0-r1 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt>
+ +sextractor-2.5.0-r1.ebuild -sextractor-2.5.0.ebuild
+ -sextractor-2.4.4.ebuild: removed flag filtering, cleaning,
+ removed old versions.
+
+*sextractor-2.5.0 (06 Sep 2006)
+
+ 06 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> +sextractor-2.5.0.ebuild:
+ Version bump.
+
+*sextractor-2.4.4 (27 Nov 2005)
+
+ 26 Nov 2005; Sebastien Fabbro <seb@ist.utl.pt> +sextractor-2.4.4.ebuild:
+ Initial import. Close bug #65684
+
diff --git a/sci-astronomy/sextractor/Manifest b/sci-astronomy/sextractor/Manifest
new file mode 100644
index 000000000..3c336634f
--- /dev/null
+++ b/sci-astronomy/sextractor/Manifest
@@ -0,0 +1,4 @@
+DIST sextractor-2.5.0.tar.gz 2321708 RMD160 336e3a47f57416ad50bbbdd2afb4ff7e858556d0 SHA1 84e111ea0796428d9336de7add3820575fd7d4cb SHA256 786f987818546d9b72fea7e786f040b63e31fbc46325deb58929251065573303
+EBUILD sextractor-2.5.0-r1.ebuild 1163 RMD160 328a5ee10e4e376f62a4ba9a0ae0454076b0f37f SHA1 b23d9636808717f3efbc1f24b111c7ea78a59895 SHA256 7cbcb59ab0b5387b6c744544772501fc0ea58879296e796ddd63c38c026c498e
+MISC ChangeLog 937 RMD160 54da2bfecc18b186fd33624caabcdea6bd621ce1 SHA1 4d6863d7c0aa62eec2b8d76fa6d7b2a67a25ddaa SHA256 5ab04874bbd2f07b929637b1bedded6938b98fef555044da2e743e7b4cdc5a75
+MISC metadata.xml 543 RMD160 8b6f4b17ec88b648a25b6a45cc07aa62b8530e6a SHA1 c85e639d87aae9e2b94fe1f67f5ffa724e080374 SHA256 45445f0c002e393359b2d580ea0f0d991b15cb01c829e6d0c1ead8e53e6bc1dc
diff --git a/sci-astronomy/sextractor/metadata.xml b/sci-astronomy/sextractor/metadata.xml
new file mode 100644
index 000000000..cd5cd149f
--- /dev/null
+++ b/sci-astronomy/sextractor/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+SExtractor (Source Extractor) is a program that builds a catalogue of
+objects from an astronomical image. Although it is particularly
+oriented towards reduction of large scale galaxy-survey data, it
+performs rather well on moderately crowded star fields. It has the
+ability to automatically separate stars and galaxy using neural
+networks.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/sextractor/sextractor-2.5.0-r1.ebuild b/sci-astronomy/sextractor/sextractor-2.5.0-r1.ebuild
new file mode 100644
index 000000000..5c4200427
--- /dev/null
+++ b/sci-astronomy/sextractor/sextractor-2.5.0-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit toolchain-funcs flag-o-matic
+
+DESCRIPTION="Extract catalogs of sources from astronomical FITS images."
+HOMEPAGE="http://terapix.iap.fr/soft/sextractor"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+DEPEND=""
+RESTRICT="test"
+
+src_compile() {
+ CONFDIR=/usr/share/${PN}/config
+ # change default configuration files location from current dir
+ sed -i -e "s:default\.:${CONFDIR}/default\.:" src/preflist.h
+ # buggy with >= O2
+ replace-flags -O[2-9] -O1
+ local myconf
+ [[ "$(tc-getCC)" == "icc" ]] \
+ && myconf="${myconf} --enable-icc"
+ econf "${myconf}" || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install () {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS BUGS ChangeLog HISTORY README THANKS
+ insinto ${CONFDIR}
+ doins config/*
+ if use doc; then
+ insinto /usr/share/doc/${PF}
+ doins doc/*
+ fi
+}
+
+pkg_postinst() {
+ elog "SExtractor configuration files are located"
+ elog "in ${CONFDIR} and loaded by default."
+}
diff --git a/sci-astronomy/skycat/ChangeLog b/sci-astronomy/skycat/ChangeLog
new file mode 100644
index 000000000..abdd60576
--- /dev/null
+++ b/sci-astronomy/skycat/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-astronomy/skycat
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*skycat-3.0.1 (14 Sep 2006)
+
+ 14 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> +skycat-3.0.1.ebuild:
+ +metadata.xml,
+ +files/skycat-3.0.1-m4.patch,
+ +files/skycat-3.0.1-gcc41.patch
+ Initial import. Closes bug #65665.
+
diff --git a/sci-astronomy/skycat/Manifest b/sci-astronomy/skycat/Manifest
new file mode 100644
index 000000000..f37338af6
--- /dev/null
+++ b/sci-astronomy/skycat/Manifest
@@ -0,0 +1,6 @@
+AUX skycat-3.0.1-gcc41.patch 14240 RMD160 950963538e531fb593c9019fcd967bde97d1252c SHA1 9d3e184de66966a988a659938eda8cd93755f409 SHA256 9dacdc5dbfc527d7642078ed01b7da3cf035af54e97b1a522705ad21685e3fc5
+AUX skycat-3.0.1-m4.patch 4816 RMD160 c142a289446d7c6fbedd15e384d9039a44d389d6 SHA1 2a0a5296f3a59fc5e1c314ab50ac8977b8af937c SHA256 daae999f2d7dbd144ff212e0be86aef98919b9daa159326d8ed6fd44b9d6f576
+DIST skycat-3.0.1.tar.gz 3175379 RMD160 38abe19c590b7b2413a749024df9f5136d701008 SHA1 89d2417915ca59934baa491b039137ab32208af0 SHA256 cfaede46a125adebe61af84c9fb0ac89b3d450d748915ee7761678df6c48b884
+EBUILD skycat-3.0.1.ebuild 1085 RMD160 9a04162806bd595d3d91daa6aa2ba1f7a06defee SHA1 0064298d5eefe6d46bb6402daa65da1c2f2e0522 SHA256 2c30c743540b0cd8ca4423796d8d6c95e96799c1f0c3f55d874f5f872f1e7034
+MISC ChangeLog 344 RMD160 39f85b16e2549ae48a5bcd1454311a76ed13ae12 SHA1 4e5115186c63a7ec90607a95d54574d7fb841783 SHA256 fe66be2d39228623bae6381983cb2ec1ece60ed2dde160fe0c23ad0060828432
+MISC metadata.xml 380 RMD160 481c8ad8d384727eb398f748140b4a1c38519b25 SHA1 7eae9ff4ee349657cb1ef1233605e60a5670af06 SHA256 ddcee971b362bdc562b112d6d2857cd9634156c17ac2e33e07e83e9ff40c4754
diff --git a/sci-astronomy/skycat/files/skycat-3.0.1-gcc41.patch b/sci-astronomy/skycat/files/skycat-3.0.1-gcc41.patch
new file mode 100644
index 000000000..0bd7b0750
--- /dev/null
+++ b/sci-astronomy/skycat/files/skycat-3.0.1-gcc41.patch
@@ -0,0 +1,384 @@
+diff -Nur skycat-3.0.1/astrotcl/generic/Fits_IO.h skycat-3.0.1.new/astrotcl/generic/Fits_IO.h
+--- skycat-3.0.1/astrotcl/generic/Fits_IO.h 2006-01-12 16:43:52.000000000 +0000
++++ skycat-3.0.1.new/astrotcl/generic/Fits_IO.h 2006-09-14 11:34:20.000000000 +0100
+@@ -49,7 +49,7 @@
+ // extend the size of the FITS header by one header block
+ int extendHeader();
+
+- static void* FitsIO::reallocFile(void* p, size_t newsize);
++ static void* reallocFile(void* p, size_t newsize);
+
+ protected:
+ // Check that this object represents a FITS file (and not just some kind of memory)
+diff -Nur skycat-3.0.1/rtd/generic/ImageData.h skycat-3.0.1.new/rtd/generic/ImageData.h
+--- skycat-3.0.1/rtd/generic/ImageData.h 2006-01-12 16:39:00.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/ImageData.h 2006-09-14 11:36:42.000000000 +0100
+@@ -348,16 +348,16 @@
+ int getSpectrum(double* xyvalues, int x0, int y0, int x1, int y1);
+
+ // get meander coords of a horizontal line at position y (index starting at 0)
+- int ImageData::getXline4(int y, int x0, int x1, double *xyvalues);
++ int getXline4(int y, int x0, int x1, double *xyvalues);
+
+ // same as getXline4 but with specified x ranges (start xr0, delta dxr)
+- int ImageData::getXline4(int y, int x0, int x1, double *xyvalues, double xr0, double dxr);
++ int getXline4(int y, int x0, int x1, double *xyvalues, double xr0, double dxr);
+
+ // get meander coords of a vertical line at position x (index starting at 0)
+- int ImageData::getYline4(int x, int y0, int y1, double *xyvalues);
++ int getYline4(int x, int y0, int y1, double *xyvalues);
+
+ // Return the image coords of the visible image area (bounding box)
+- void ImageData::getBbox(double *x0, double *x1, double *y0, double *y1);
++ void getBbox(double *x0, double *x1, double *y0, double *y1);
+
+ // get min and max values of an image area
+ int getMinMax(double rx0, double ry0, int w, int h, double *minval, double *maxval);
+diff -Nur skycat-3.0.1/rtd/generic/ImageDisplay.h skycat-3.0.1.new/rtd/generic/ImageDisplay.h
+--- skycat-3.0.1/rtd/generic/ImageDisplay.h 2006-01-12 16:39:29.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/ImageDisplay.h 2006-09-14 11:35:30.000000000 +0100
+@@ -78,7 +78,7 @@
+ }
+
+ // flush X output buffer
+- void ImageDisplay::flushX();
++ void flushX();
+
+ // other info
+ int width() {return xImage_ ? xImage_->width : 0;}
+diff -Nur skycat-3.0.1/rtd/generic/RtdCamera.h skycat-3.0.1.new/rtd/generic/RtdCamera.h
+--- skycat-3.0.1/rtd/generic/RtdCamera.h 2006-01-12 16:39:14.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/RtdCamera.h 2006-09-14 11:39:21.000000000 +0100
+@@ -48,7 +48,7 @@
+ public:
+
+ // constructor
+- RtdCamera::RtdCamera(
++ RtdCamera(
+ const char* name,
+ Tcl_Interp*,
+ int verbose,
+@@ -56,64 +56,64 @@
+ char* image = "RtdCamera");
+
+ // destructor
+- virtual RtdCamera::~RtdCamera();
++ virtual ~RtdCamera();
+
+ // static file handler, called by Tk file handler for realtime image events
+- static void RtdCamera::fileEventProc(ClientData, int mask);
++ static void fileEventProc(ClientData, int mask);
+
+ // start/stop/pause or continue accepting images
+- int RtdCamera::start(const char* cameraName);
+- int RtdCamera::stop();
+- int RtdCamera::pause();
+- int RtdCamera::cont();
++ int start(const char* cameraName);
++ int stop();
++ int pause();
++ int cont();
+
+ // return camera name
+- char* RtdCamera::camera() {return camera_;}
++ char* camera() {return camera_;}
+
+ // Add timestamp in performance tool.
+- void RtdCamera::timeStamp(char *evDesc);
++ void timeStamp(char *evDesc);
+
+ // update global variables
+- int RtdCamera::updateGlobals();
++ int updateGlobals();
+
+ // check if camera is attached
+- int RtdCamera::attached();
++ int attached();
+
+ protected:
+
+ // member called by fileEventProc for image events
+- int RtdCamera::fileEvent();
++ int fileEvent();
+
+ // cleanup image events in the socket queue
+- void RtdCamera::cleanup();
++ void cleanup();
+
+ // called to display new image from shared memory
+ // (defined in a derived class)
+- virtual int RtdCamera::display(const rtdIMAGE_INFO&, const Mem& data) = 0;
++ virtual int display(const rtdIMAGE_INFO&, const Mem& data) = 0;
+
+ // set camera name
+- void RtdCamera::camera(const char *camera) {strcpy(camBuf_, camera);}
++ void camera(const char *camera) {strcpy(camBuf_, camera);}
+
+ // create/delete the Tcl file handler
+- void RtdCamera::fileHandler(int create);
++ void fileHandler(int create);
+
+ // disconnect from camera
+- void RtdCamera::disconnect();
++ void disconnect();
+
+ // Decrement the semaphore
+- void RtdCamera::semDecr();
++ void semDecr();
+
+ // check if rtdServer is alive
+- void RtdCamera::rtdServerCheck();
++ void rtdServerCheck();
+
+ // check status after image event failure
+- void RtdCamera::checkStat();
++ void checkStat();
+
+ // start accepting events from the camera
+- int RtdCamera::attach(const char* camera);
++ int attach(const char* camera);
+
+ // check image type
+- int RtdCamera::checkType(int type);
++ int checkType(int type);
+
+ Tcl_Interp* interp_; // Tcl interp (for file events, error handling)
+ rtdIMAGE_EVT_HNDL* eventHndl_; // image event handle
+@@ -133,9 +133,9 @@
+
+ // -- short cuts --
+
+- int RtdCamera::connected() {return connected_;}
+- void RtdCamera::connected(int set) {connected_ = set; }
+- void RtdCamera::attached(int set) {attached_ = set; }
++ int connected() {return connected_;}
++ void connected(int set) {connected_ = set; }
++ void attached(int set) {attached_ = set; }
+ };
+
+ #endif /* _RtdCamera_h_ */
+diff -Nur skycat-3.0.1/rtd/generic/RtdImage.h skycat-3.0.1.new/rtd/generic/RtdImage.h
+--- skycat-3.0.1/rtd/generic/RtdImage.h 2006-01-12 16:39:28.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/RtdImage.h 2006-09-14 11:47:08.000000000 +0100
+@@ -428,7 +428,7 @@
+ static int rtd_set_cmap(ClientData, Tcl_Interp* interp, int argc, char** argv);
+
+ // update idle tasks and performance test variables
+- void RtdImage::updateRequests();
++ void updateRequests();
+
+ // read-only access to configuration options
+ static ImageColor* colors() {return colors_;}
+diff -Nur skycat-3.0.1/rtd/generic/RtdPerf.h skycat-3.0.1.new/rtd/generic/RtdPerf.h
+--- skycat-3.0.1/rtd/generic/RtdPerf.h 2006-01-12 16:39:21.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/RtdPerf.h 2006-09-14 11:40:28.000000000 +0100
+@@ -23,42 +23,42 @@
+
+ public:
+ // Constructor
+- RtdPerf::RtdPerf(Tcl_Interp* interp);
++ RtdPerf(Tcl_Interp* interp);
+
+ // Destructor
+- RtdPerf::~RtdPerf();
++ ~RtdPerf();
+
+ // Add delta time to 'timevar'
+- void RtdPerf::timeInc(double *timevar);
++ void timeInc(double *timevar);
+
+ // Start a new cycle
+- void RtdPerf::newCycle();
++ void newCycle();
+
+ // End a cycle and set the Tcl global variables
+- void RtdPerf::endCycle();
++ void endCycle();
+
+ // Reset the time variables and Tcl global variables
+- void RtdPerf::reset();
++ void reset();
+
+ // Switch performance test on
+- void RtdPerf::on() {maybeOn_ = 1; on_ = 0;}
+- void RtdPerf::on(int set) {on_ = set;}
++ void on() {maybeOn_ = 1; on_ = 0;}
++ void on(int set) {on_ = set;}
+
+ // Switch performance test on
+- void RtdPerf::off() {maybeOn_ = 0; on_ = 0;}
++ void off() {maybeOn_ = 0; on_ = 0;}
+
+ // Set verbose and debug flag
+- void RtdPerf::verbose(int set) {verbose_ = set;}
+- void RtdPerf::debug(int set) {debug_ = set;}
++ void verbose(int set) {verbose_ = set;}
++ void debug(int set) {debug_ = set;}
+
+ // Set the instance name of the RtdImage (used for global Tcl variables)
+- void RtdPerf::name(char *nam) {strcpy(name_, nam);}
++ void name(char *nam) {strcpy(name_, nam);}
+
+ // -- short cuts --
+
+- void RtdPerf::GENtime() {timeInc(&GENtime_);}
+- void RtdPerf::TCLtime() {timeInc(&TCLtime_);}
+- void RtdPerf::Xtime() {timeInc(&Xtime_);}
++ void GENtime() {timeInc(&GENtime_);}
++ void TCLtime() {timeInc(&TCLtime_);}
++ void Xtime() {timeInc(&Xtime_);}
+
+ protected:
+ RtdDebugLog *dbl_; // debug log object
+@@ -84,9 +84,9 @@
+
+ // -- short cuts --
+
+- char* RtdPerf::name() {return(name_);}
+- int RtdPerf::isOn() {return on_;}
+- int RtdPerf::maybeOn() {return maybeOn_;}
++ char* name() {return(name_);}
++ int isOn() {return on_;}
++ int maybeOn() {return maybeOn_;}
+ };
+
+ #endif /* _RtdPerf_h_ */
+diff -Nur skycat-3.0.1/rtd/generic/RtdUtils.h skycat-3.0.1.new/rtd/generic/RtdUtils.h
+--- skycat-3.0.1/rtd/generic/RtdUtils.h 2006-01-12 16:39:16.000000000 +0000
++++ skycat-3.0.1.new/rtd/generic/RtdUtils.h 2006-09-14 11:37:32.000000000 +0100
+@@ -28,11 +28,11 @@
+ class RtdDebugLog {
+ public:
+
+- RtdDebugLog::RtdDebugLog(char *nam, int debug);
++ RtdDebugLog(char *nam, int debug);
+
+- void RtdDebugLog::log(const char *format, ...);
+- void RtdDebugLog::setlog(int set) {debug_ = set;}
+- int RtdDebugLog::setlog() {return debug_;}
++ void log(const char *format, ...);
++ void setlog(int set) {debug_ = set;}
++ int setlog() {return debug_;}
+
+ protected:
+ char name_[100]; // name of application
+diff -Nur skycat-3.0.1/rtd/rtdevt/rtdCLNT.h skycat-3.0.1.new/rtd/rtdevt/rtdCLNT.h
+--- skycat-3.0.1/rtd/rtdevt/rtdCLNT.h 2006-01-12 16:40:00.000000000 +0000
++++ skycat-3.0.1.new/rtd/rtdevt/rtdCLNT.h 2006-09-14 11:51:56.000000000 +0100
+@@ -40,52 +40,52 @@
+ ~rtdCLNT();
+
+ // store/return the name of the requestor
+- char *rtdCLNT::ReqName() { return reqName_; }
+- void rtdCLNT::ReqName(char *name) { strncpy (reqNameBuf_, name, RTD_NAMELEN); }
++ char *ReqName() { return reqName_; }
++ void ReqName(char *name) { strncpy (reqNameBuf_, name, RTD_NAMELEN); }
+
+ // store/return the name of the camera
+- char *rtdCLNT::CamName() { return camName_; }
+- void rtdCLNT::CamName(char *name) { strncpy (camNameBuf_, name, RTD_NAMELEN); }
++ char *CamName() { return camName_; }
++ void CamName(char *name) { strncpy (camNameBuf_, name, RTD_NAMELEN); }
+
+ // store/return the name of the socket file descriptor
+- int rtdCLNT::Socket() { return socket_; }
+- void rtdCLNT::Socket(int socket) { socket_ = socket; }
++ int Socket() { return socket_; }
++ void Socket(int socket) { socket_ = socket; }
+
+ // return the semaphore params set by the requestor
+- int rtdCLNT::semId() { return semId_; }
++ int semId() { return semId_; }
+
+ // return the number of semaphores
+- int rtdCLNT::shmNum() { return shmNum_; }
++ int shmNum() { return shmNum_; }
+
+ // set the values for semId and shmNum
+- void rtdCLNT::SetSemPar(int semId, int shmNum);
++ void SetSemPar(int semId, int shmNum);
+
+ // store/return the index
+- int rtdCLNT::Index() { return index_; }
+- void rtdCLNT::Index(int index) { index_ = index; }
++ int Index() { return index_; }
++ void Index(int index) { index_ = index; }
+
+ // store/return the port number
+- int rtdCLNT::Port() { return port_; }
+- void rtdCLNT::Port(int port) { port_ = port; }
++ int Port() { return port_; }
++ void Port(int port) { port_ = port; }
+
+ // store/return the type number
+- int rtdCLNT::Type() { return type_; }
+- void rtdCLNT::Type(int type) { type_ = type; }
++ int Type() { return type_; }
++ void Type(int type) { type_ = type; }
+
+ // clear a buffer
+- void rtdCLNT::BufClear(char *name) { memset (name, '\0', RTD_NAMELEN); }
++ void BufClear(char *name) { memset (name, '\0', RTD_NAMELEN); }
+
+ // are we attched?
+- int rtdCLNT::Attached() { return (*reqName_ == '\0' || *camName_ == '\0'); }
++ int Attached() { return (*reqName_ == '\0' || *camName_ == '\0'); }
+
+- void rtdCLNT::Attach(char* reqName, char *camName);
+- void rtdCLNT::Detach();
++ void Attach(char* reqName, char *camName);
++ void Detach();
+
+- int rtdCLNT::Forward(rtdPACKET *rtdPacket);
+- void rtdCLNT::Cleanup();
+- int rtdCLNT::Accept(int listenSocket);
+- int rtdCLNT::AttachedToCamera(char *camera);
+- char *rtdCLNT::TypeName();
++ int Forward(rtdPACKET *rtdPacket);
++ void Cleanup();
++ int Accept(int listenSocket);
++ int AttachedToCamera(char *camera);
++ char *TypeName();
+
+ private:
+ char *reqName_; // name of requestor
+diff -Nur skycat-3.0.1/rtd/rtdevt/rtdLOG.h skycat-3.0.1.new/rtd/rtdevt/rtdLOG.h
+--- skycat-3.0.1/rtd/rtdevt/rtdLOG.h 2006-01-12 16:39:54.000000000 +0000
++++ skycat-3.0.1.new/rtd/rtdevt/rtdLOG.h 2006-09-14 11:51:06.000000000 +0100
+@@ -24,8 +24,8 @@
+ rtdLOG(int);
+ ~rtdLOG();
+
+- void rtdLOG::log(const char *format, ...);
+- int rtdLOG::Verbose() { return verbose_; }
++ void log(const char *format, ...);
++ int Verbose() { return verbose_; }
+
+ private:
+ int verbose_;
+diff -Nur skycat-3.0.1/rtd/rtdevt/rtdSERVER.h skycat-3.0.1.new/rtd/rtdevt/rtdSERVER.h
+--- skycat-3.0.1/rtd/rtdevt/rtdSERVER.h 2006-01-12 16:39:57.000000000 +0000
++++ skycat-3.0.1.new/rtd/rtdevt/rtdSERVER.h 2006-09-14 11:52:24.000000000 +0100
+@@ -39,15 +39,15 @@
+ rtdSERVER(int, int, int);
+ ~rtdSERVER();
+
+- int rtdSERVER::Loop();
++ int Loop();
+
+ protected:
+- rtdCLNT *rtdSERVER::GetCurrClient();
+- void rtdSERVER::ServImageCmd(rtdPACKET *rtdPacket);
+- void rtdSERVER::ServStatusCmd(int socket);
+- int rtdSERVER::IncrSem(rtdPACKET *rtdPacket, int increment);
+- rtdCLNT *rtdSERVER::Accept();
+- void rtdSERVER::DisconnectClient(rtdCLNT *client);
++ rtdCLNT *GetCurrClient();
++ void ServImageCmd(rtdPACKET *rtdPacket);
++ void ServStatusCmd(int socket);
++ int IncrSem(rtdPACKET *rtdPacket, int increment);
++ rtdCLNT *Accept();
++ void DisconnectClient(rtdCLNT *client);
+
+ private:
+ int socketFd_; // listen socket
diff --git a/sci-astronomy/skycat/files/skycat-3.0.1-m4.patch b/sci-astronomy/skycat/files/skycat-3.0.1-m4.patch
new file mode 100644
index 000000000..4a3bfc213
--- /dev/null
+++ b/sci-astronomy/skycat/files/skycat-3.0.1-m4.patch
@@ -0,0 +1,141 @@
+--- skycat-3.0.1/tclconfig/tcl.m4 2006-02-01 22:10:36.000000000 +0000
++++ skycat-3.0.1.new/tclconfig/tcl.m4 2006-09-14 11:23:20.000000000 +0100
+@@ -731,6 +731,50 @@
+ ])
+
+ #--------------------------------------------------------------------
++# TEA_CONFIG_SYSTEM
++#
++# Determine what the system is (some things cannot be easily checked
++# on a feature-driven basis, alas). This can usually be done via the
++# "uname" command, but there are a few systems, like Next, where
++# this doesn't work.
++#
++# Arguments:
++# none
++#
++# Results:
++# Defines the following var:
++#
++# system - System/platform/version identification code.
++#
++#--------------------------------------------------------------------
++
++AC_DEFUN(TEA_CONFIG_SYSTEM, [
++ AC_MSG_CHECKING([system version])
++ AC_CACHE_VAL(tcl_cv_sys_version,[
++ if test -f /usr/lib/NextStep/software_version; then
++ tcl_cv_sys_version=NEXTSTEP-`awk '/3/,/3/' /usr/lib/NextStep/software_version`
++ else
++ tcl_cv_sys_version=`uname -s`-`uname -r`
++ if test "$?" -ne 0 ; then
++ AC_MSG_WARN([can't find uname command])
++ tcl_cv_sys_version=unknown
++ else
++ # Special check for weird MP-RAS system (uname returns weird
++ # results, and the version is kept in special file).
++
++ if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
++ tcl_cv_sys_version=MP-RAS-`awk '{print $3}' /etc/.relid`
++ fi
++ if test "`uname -s`" = "AIX" ; then
++ tcl_cv_sys_version=AIX-`uname -v`.`uname -r`
++ fi
++ fi
++ fi])
++ AC_MSG_RESULT($tcl_cv_sys_version)
++ system=$tcl_cv_sys_version
++])
++
++#--------------------------------------------------------------------
+ # TEA_CONFIG_CFLAGS
+ #
+ # Try to determine the proper flags to pass to the compiler
+@@ -849,30 +893,7 @@
+ # for the system. This can usually be done via the "uname" command, but
+ # there are a few systems, like Next, where this doesn't work.
+
+- AC_MSG_CHECKING([system version (for dynamic loading)])
+- if test -f /usr/lib/NextStep/software_version; then
+- system=NEXTSTEP-`awk '/3/,/3/' /usr/lib/NextStep/software_version`
+- else
+- system=`uname -s`-`uname -r`
+- if test "$?" -ne 0 ; then
+- AC_MSG_RESULT([unknown (can't find uname command)])
+- system=unknown
+- else
+- # Special check for weird MP-RAS system (uname returns weird
+- # results, and the version is kept in special file).
+-
+- if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
+- fi
+- if test "`uname -s`" = "AIX" ; then
+- system=AIX-`uname -v`.`uname -r`
+- fi
+- if test "${TEA_PLATFORM}" = "windows" ; then
+- system=windows
+- fi
+- AC_MSG_RESULT([$system])
+- fi
+- fi
++ TEA_CONFIG_SYSTEM
+
+ # Step 2: check for existence of -ldl library. This is needed because
+ # Linux can use either -ldl or -ldld for dynamic loading.
+@@ -2318,25 +2339,8 @@
+ AC_DEFUN(TEA_BLOCKING_STYLE, [
+ AC_CHECK_HEADERS(sys/ioctl.h)
+ AC_CHECK_HEADERS(sys/filio.h)
++ TEA_CONFIG_SYSTEM
+ AC_MSG_CHECKING([FIONBIO vs. O_NONBLOCK for nonblocking I/O])
+- if test -f /usr/lib/NextStep/software_version; then
+- system=NEXTSTEP-`awk '/3/,/3/' /usr/lib/NextStep/software_version`
+- else
+- system=`uname -s`-`uname -r`
+- if test "$?" -ne 0 ; then
+- system=unknown
+- else
+- # Special check for weird MP-RAS system (uname returns weird
+- # results, and the version is kept in special file).
+-
+- if test -r /etc/.relid -a "X`uname -n`" = "X`uname -s`" ; then
+- system=MP-RAS-`awk '{print $3}' /etc/.relid'`
+- fi
+- if test "`uname -s`" = "AIX" ; then
+- system=AIX-`uname -v`.`uname -r`
+- fi
+- fi
+- fi
+ case $system in
+ # There used to be code here to use FIONBIO under AIX. However, it
+ # was reported that FIONBIO doesn't work under AIX 3.2.5. Since
+@@ -3031,13 +3035,13 @@
+ fi
+ if test "${exec_prefix}" = "NONE" -a x"${prefix_default}" = x"yes" \
+ -o x"${exec_prefix_default}" = x"yes" ; then
+- #if test x"${TCL_EXEC_PREFIX}" != x; then
+- #AC_MSG_NOTICE([--exec-prefix defaulting to TCL_EXEC_PREFIX ${TCL_EXEC_PREFIX}])
+- #exec_prefix=${TCL_EXEC_PREFIX}
+- #else
++ if test x"${TCL_EXEC_PREFIX}" != x; then
++ AC_MSG_NOTICE([--exec-prefix defaulting to TCL_EXEC_PREFIX ${TCL_EXEC_PREFIX}])
++ exec_prefix=${TCL_EXEC_PREFIX}
++ else
+ AC_MSG_NOTICE([--exec-prefix defaulting to ${prefix}])
+ exec_prefix=$prefix
+- #fi
++ fi
+ fi
+ ])
+
+@@ -3817,7 +3821,8 @@
+
+ # check in a few common install locations
+ if test x"${ac_cv_c_$1config}" = x ; then
+- for i in `ls -d ${exec_prefix}/lib 2>/dev/null` \
++ for i in `ls -d ${libdir} 2>/dev/null` \
++ `ls -d ${exec_prefix}/lib 2>/dev/null` \
+ `ls -d ${prefix}/lib 2>/dev/null` \
+ `ls -d /usr/local/lib 2>/dev/null` \
+ `ls -d /usr/contrib/lib 2>/dev/null` \
diff --git a/sci-astronomy/skycat/metadata.xml b/sci-astronomy/skycat/metadata.xml
new file mode 100644
index 000000000..c78fd22c4
--- /dev/null
+++ b/sci-astronomy/skycat/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ SkyCat is a tool that combines visualization of images and access
+ to catalogs and archive data for astronomy. It was developed at
+ the European Southern Observatory.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/skycat/skycat-3.0.1.ebuild b/sci-astronomy/skycat/skycat-3.0.1.ebuild
new file mode 100644
index 000000000..cb9b07636
--- /dev/null
+++ b/sci-astronomy/skycat/skycat-3.0.1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit autotools
+
+DESCRIPTION="ESO astronomical image visualizer with catalog access."
+HOMEPAGE="http://archive.eso.org/skycat"
+SRC_URI="ftp://ftp.eso.org/pub/archive/${PN}/Sources/${P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+IUSE="threads"
+
+DEPEND=">=dev-tcltk/tclx-2.4
+ >=dev-tcltk/blt-2.4
+ >=dev-tcltk/itcl-3.3
+ >=dev-tcltk/iwidgets-4.0.1
+ >=dev-tcltk/tkimg-1.3"
+
+
+src_unpack() {
+ unpack ${A}
+ # fix buggy tcl.m4 for bash3
+ epatch "${FILESDIR}"/${P}-m4.patch
+ # fix old style headers, set as error by new g++
+ epatch "${FILESDIR}"/${P}-gcc41.patch
+ cd "${S}"
+ eautoreconf
+}
+
+src_compile() {
+ econf \
+ $(use_enable threads) \
+ || die "econf failed"
+ emake
+ # a second time to make sure every dir passed
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc README CHANGES VERSION
+ for d in tclutil astrotcl rtd cat skycat; do
+ docinto ${d}
+ dodoc README CHANGES VERSION
+ done
+}
diff --git a/sci-astronomy/skymaker/ChangeLog b/sci-astronomy/skymaker/ChangeLog
new file mode 100644
index 000000000..189a83a4d
--- /dev/null
+++ b/sci-astronomy/skymaker/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-astronomy/skymaker
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 20 Apr 2007; Sébastien Fabbro <bicatali@gentoo.org> ChangeLog:
+ Initial import
+
diff --git a/sci-astronomy/skymaker/Manifest b/sci-astronomy/skymaker/Manifest
new file mode 100644
index 000000000..193f9ca25
--- /dev/null
+++ b/sci-astronomy/skymaker/Manifest
@@ -0,0 +1,4 @@
+DIST skymaker-3.1.0.tar.gz 409089 RMD160 f40c969fc4de0f42240f381c003bc365f121f5cc SHA1 21c230ee2c2ebe0cf881be0efa1e701641e480fc SHA256 a61fbd31e3eb7bc1387018d6d1eb719503215d23027fa8919d8bbe4e805ab5e4
+EBUILD skymaker-3.1.0.ebuild 853 RMD160 4a7567b16a863f72dfa1a137b764a92c645babb7 SHA1 2ea54b5f22893595b82135bc9de5a6a69489a70e SHA256 fd3b8a674f8ad7d616f7f3231774ac1e40c3c2536f305025f5de8801ef6ac60f
+MISC ChangeLog 207 RMD160 a006be2e6d1baa2998c22d252d2330b9aa568985 SHA1 a351147734a8997886dfa5ba68e265c70e532118 SHA256 d69f4c4f847cf80cf62b68fc87e2369401e334ce9f2a61d5edd313b5f3dab209
+MISC metadata.xml 522 RMD160 82a2f56adf45447226214d63b733d5ee59a7a28f SHA1 f3fd9b95737eec4ac3bb5d7103b6237b21089d20 SHA256 d86351847a40cd61b3b7da6a9794b11a34de5192952dcb849d91cbc442b05646
diff --git a/sci-astronomy/skymaker/metadata.xml b/sci-astronomy/skymaker/metadata.xml
new file mode 100644
index 000000000..caa0b0596
--- /dev/null
+++ b/sci-astronomy/skymaker/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+SkyMaker is a program that simulates astronomical images. It accepts
+object lists in ASCII generated by the Stuff program to produce
+realistic astronomical fields. There are various options for the user:
+build a realistic Point Spread Function, generate a list of stars and
+galaxies. Galaxies are modeled analytically.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/skymaker/skymaker-3.1.0.ebuild b/sci-astronomy/skymaker/skymaker-3.1.0.ebuild
new file mode 100644
index 000000000..5054b7e51
--- /dev/null
+++ b/sci-astronomy/skymaker/skymaker-3.1.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Program that simulates astronomical images"
+HOMEPAGE="http://terapix.iap.fr/soft/skymaker"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="threads mpi"
+RESTRICT="test"
+
+DEPEND=">=sci-libs/fftw-3
+ mpi? ( virtual/mpi )"
+
+# mpi stuff untested.
+src_compile() {
+ use mpi || export MPICC="$(tc-getCC)"
+ local myconf
+ # --disable-threads is buggy
+ use threads && myconf="--enable-threads"
+ econf \
+ $(use_enable mpi) \
+ ${myconf} \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS
+}
diff --git a/sci-astronomy/stiff/ChangeLog b/sci-astronomy/stiff/ChangeLog
new file mode 100644
index 000000000..27c6f18d8
--- /dev/null
+++ b/sci-astronomy/stiff/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for sci-astronomy/stiff
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org> stiff-1.10.ebuild:
+ cleaning
+
+ 29 Dec 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ Removed icc flag, too buggy.
+
+*stiff-1.10 (19 Sep 2006)
+
+ 19 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> +stiff-1.10.ebuild:
+ Initial import.
+
diff --git a/sci-astronomy/stiff/Manifest b/sci-astronomy/stiff/Manifest
new file mode 100644
index 000000000..a052d2680
--- /dev/null
+++ b/sci-astronomy/stiff/Manifest
@@ -0,0 +1,4 @@
+DIST stiff-1.10.tar.gz 5077852 RMD160 73645df6d9b1db5d30f2400336878e5b0ba4d253 SHA1 b55b61e1238f9fb3fc8a50b85ce2b5a8d0350954 SHA256 15433e1e78e25601fc40c106108ee5021aaa9be336f29a771f1747f497561eb1
+EBUILD stiff-1.10.ebuild 552 RMD160 c1149a3c2c7aaa8a7d1ce017c9007ab85979c748 SHA1 788f356f427daa4b2946485c065f4479a7851b11 SHA256 1d1b0e66e025415218aad92c209bb78d1342f2d7db7da8f2a3c005391e0d2865
+MISC ChangeLog 405 RMD160 ede7214b4ab6ba9093ed5b39b29eb875c369f55b SHA1 ba6e1a2eddd94700b6ca48c7b3ac94ca0ae3239a SHA256 d0a593cd903d28015bbc19b35dc0810cb9003845dc3730c6d9943899a3356e89
+MISC metadata.xml 348 RMD160 808677a0e79eb338980a9cbf5d68a086593a47b0 SHA1 88a4e495e68c143b0a4243d339ae06debf0c02bd SHA256 ca1f352ed481da49dbcaeb817d9579d12b35557c9abb4bc670b2986346200e94
diff --git a/sci-astronomy/stiff/metadata.xml b/sci-astronomy/stiff/metadata.xml
new file mode 100644
index 000000000..39033f584
--- /dev/null
+++ b/sci-astronomy/stiff/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+STIFF is a program that convert scientific FITS images to the
+more popular TIFF, in 8 (grayscale) or 24 (true colour: 3 times 8) bits per
+pixel.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/stiff/stiff-1.10.ebuild b/sci-astronomy/stiff/stiff-1.10.ebuild
new file mode 100644
index 000000000..54f46b5f5
--- /dev/null
+++ b/sci-astronomy/stiff/stiff-1.10.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="Converts astronomical FITS images to the TIFF format for illustration purposes."
+HOMEPAGE="http://terapix.iap.fr/soft/stiff"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+DEPEND=""
+
+src_install () {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS BUGS ChangeLog HISTORY README THANKS
+ use doc && dodoc doc/*
+}
diff --git a/sci-astronomy/swarp/ChangeLog b/sci-astronomy/swarp/ChangeLog
new file mode 100644
index 000000000..9d7f27536
--- /dev/null
+++ b/sci-astronomy/swarp/ChangeLog
@@ -0,0 +1,31 @@
+# ChangeLog for sci-astronomy/swarp
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 14 Jan 2008; Sébastien Fabbro <bicatali@gentoo.org> -swarp-2.17.0.ebuild,
+ +swarp-2.17.1.ebuild:
+ Version bump
+
+ 09 Jan 2008; Sébastien Fabbro <bicatali@gentoo.org> +swarp-2.17.0.ebuild:
+ Version bump
+
+ 01 Aug 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ -swarp-2.16.0-r1.ebuild, +swarp-2.16.4.ebuild:
+ Version bump
+
+ 26 Mar 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ swarp-2.16.0-r1.ebuild:
+ cleaning
+
+ 29 Dec 2006; Sebastien Fabbro <seb@ist.utl.pt>;
+ Removed icc flag, too buggy.
+
+*swarp-2.16.0-r1 (15 Oct 2006)
+
+ 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt> swarp-2.16.0-r1.ebuild
+ Removed flag filtering. Some cleaning.
+
+*swarp-2.16.0 (10 Sep 2006)
+
+ 10 Sep 2006; Sebastien Fabbro <seb@ist.utl.pt> swarp-2.16.0.ebuild
+ Initial import. Close bug #65685.
diff --git a/sci-astronomy/swarp/Manifest b/sci-astronomy/swarp/Manifest
new file mode 100644
index 000000000..073c92c2c
--- /dev/null
+++ b/sci-astronomy/swarp/Manifest
@@ -0,0 +1,6 @@
+DIST swarp-2.16.4.tar.gz 3425784 RMD160 f9b88b2f6ba7694f55668ec7ea9a75c7e96bd467 SHA1 7195364e5f90f89e65b2c3519a7fe12d95ea8d57 SHA256 b58a2b842e2f8f10a851186c05fa63fbd69bc41cb65c2b537a74ec2274e5af1b
+DIST swarp-2.17.1.tar.gz 1962775 RMD160 240d23e4e49218914b816b448651b221b4f58586 SHA1 eadd57e58d3fb4255495c3e0741b1eb4a2842472 SHA256 34e815d44f3b1c3c7bfdeb01bbdcf32d1eac239527a0937c3ed2b6f7be34bcee
+EBUILD swarp-2.16.4.ebuild 900 RMD160 198d478e21ee9b5740ac5f9d5c5bab43c4be4174 SHA1 fbac9eeb1db9a2f7b51a50565026ea91921147ad SHA256 805209b501409a00f76f2d496f15feacd4c2f6ce92653f7e097e6d1c3fa7f36a
+EBUILD swarp-2.17.1.ebuild 907 RMD160 a47ac6236f96622a6e3225c80df5204823f1d284 SHA1 756a5270f1443ad92236d2238c8d17eea0b430fb SHA256 04045095618e956a18f8ca2629b646d79b3595d23ecd7e472b492b5c96e25a41
+MISC ChangeLog 909 RMD160 be55513408b56526b424d7406b057e5d2708dad4 SHA1 ae68e6855c18ffacc8e20f319605a3bb2e68f213 SHA256 5eed1b9918607b643f10760301133a4779b20d86b15586fb7118b08de53ff676
+MISC metadata.xml 302 RMD160 218ab232f609c110c3cf25aca0788e467cb9b99d SHA1 0900b05ec1dfdc906791c4fca976606078a5dfc9 SHA256 8de11d2c9a0b8f3c81195f010122b0ee86f4c5f9bac16db640bb326e42b5570b
diff --git a/sci-astronomy/swarp/metadata.xml b/sci-astronomy/swarp/metadata.xml
new file mode 100644
index 000000000..521a0577f
--- /dev/null
+++ b/sci-astronomy/swarp/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+SWarp takes astronomical FITS images with a WCS-like projection,
+resample and coadd them together.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-astronomy/swarp/swarp-2.16.4.ebuild b/sci-astronomy/swarp/swarp-2.16.4.ebuild
new file mode 100644
index 000000000..23852d094
--- /dev/null
+++ b/sci-astronomy/swarp/swarp-2.16.4.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit toolchain-funcs
+
+DESCRIPTION="Resample and coadd astronomical FITS images"
+HOMEPAGE="http://terapix.iap.fr/soft/swarp"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc threads mpi"
+RDEPEND="mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}"
+
+# mpi stuff untested.
+src_compile() {
+ use mpi || export MPICC="$(tc-getCC)"
+ local myconf
+ # --disable-threads is buggy
+ use threads && myconf="--enable-threads"
+ econf \
+ $(use_enable mpi) \
+ ${myconf} \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS
+ if use doc; then
+ insinto /usr/share/doc/${PF}
+ doins doc/*
+ fi
+}
diff --git a/sci-astronomy/swarp/swarp-2.17.1.ebuild b/sci-astronomy/swarp/swarp-2.17.1.ebuild
new file mode 100644
index 000000000..9e7fd7185
--- /dev/null
+++ b/sci-astronomy/swarp/swarp-2.17.1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit toolchain-funcs
+
+DESCRIPTION="Resample and coadd astronomical FITS images"
+HOMEPAGE="http://terapix.iap.fr/soft/swarp"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/bertin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc threads mpi"
+RDEPEND="mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}"
+
+# mpi stuff untested.
+src_compile() {
+ use mpi || export MPICC="$(tc-getCC)"
+ local myconf
+ # --disable-threads is buggy
+ use threads && myconf="--enable-threads"
+ econf \
+ $(use_enable mpi) \
+ ${myconf} \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS || die
+ if use doc; then
+ insinto /usr/share/doc/${PF}
+ doins doc/*
+ fi
+}
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
new file mode 100644
index 000000000..2ae77445a
--- /dev/null
+++ b/sci-biology/amos/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/amos
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> ChangeLog:
+ Mass import from sunrise
+
+ 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> amos-2.0.2.ebuild:
+ fix die messages
+
+ 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +amos-2.0.2.ebuild, +metadata.xml:
+ new package (bug 175293)
+
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
new file mode 100644
index 000000000..33e773f6e
--- /dev/null
+++ b/sci-biology/amos/Manifest
@@ -0,0 +1,4 @@
+DIST amos-2.0.2.tar.gz 1822049 RMD160 6cf5f6afbc98494a9799fce678cab7f24a5c9d0d SHA1 de49a1f89b0a4ee994add23bdabe5841bcff6d68 SHA256 1bffa59ffe35a26f8328d49ac94df9f0f1be0c324954fd53f041c63353272416
+EBUILD amos-2.0.2.ebuild 605 RMD160 c2a5f45a542647d5460f5aa52eae46a9e44e7cc6 SHA1 bc2294caaacfba02e012d76ee1971fb5344ce4b9 SHA256 fa2320d424535504edd64a82be5bd9104ec981b1ec6e051de4c21d3f5ac8d8ae
+MISC ChangeLog 420 RMD160 21fed08e83092846b647b550c24b9ff5e0827b9a SHA1 0e1129d82c9b41196c5446f30950b99b07c08b91 SHA256 a8825ccc7fb112030924858a10106305ee797c008ef9751846264316f2479838
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/amos/amos-2.0.2.ebuild b/sci-biology/amos/amos-2.0.2.ebuild
new file mode 100644
index 000000000..23584bbc0
--- /dev/null
+++ b/sci-biology/amos/amos-2.0.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit qt3
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="$(qt_min_version 3.3)"
+RDEPEND="${DEPEND}
+ sci-biology/mummer"
+
+src_compile() {
+ econf || die "econf failed"
+ # TODO: fix parallel make. Notified upstream
+ emake -j1 || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/amos/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/blat/ChangeLog b/sci-biology/blat/ChangeLog
new file mode 100644
index 000000000..2b7ceafad
--- /dev/null
+++ b/sci-biology/blat/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/blat
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 30 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blat-34.ebuild:
+ version bump!
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blat-33.ebuild:
+ Mass import from sunrise
+
+ 05 Oct 2006; Markus Ullmann <jokey@gentoo.org> blat-33.ebuild:
+ Small QA
+
+ 25 Sep 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx> +blat-33.ebuild,
+ +metadata.xml:
+ new ebuild: sci-biology/blat-33 (bug 135307)
+
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
new file mode 100644
index 000000000..c9dba2ecd
--- /dev/null
+++ b/sci-biology/blat/Manifest
@@ -0,0 +1,6 @@
+DIST blatSrc33.zip 1308517 RMD160 76d7f8f713a5ece72c63eb8852662acf83e2e736 SHA1 a9606455549e2f153ab04321d08e59f60c039dd2 SHA256 4ca932721f529d815e64b51940c94d8136faec52c6b8bf8c3fcd3706337d9a29
+DIST blatSrc34.zip 2142975 RMD160 6c8226305c56ea56504103db6ef401841bc0c6f7 SHA1 4208451b5fa5f6cf30d15afb1df79edc850735db SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
+EBUILD blat-33.ebuild 812 RMD160 bcc1c8d50d708410dcc1e9bfd650523806209d6b SHA1 851fb369c0d328c3c1add9b94c66aae24fa66bfa SHA256 c80f630e4df9309dbfc599247a04128605a635cccec1c5ec2bf6b02d0f998b2e
+EBUILD blat-34.ebuild 887 RMD160 acd8641037ab23c784c54bacf4a8e7213953040d SHA1 e152207366ca8608b75a3c5f921e786938f80576 SHA256 918f6fbc8a6ec60f2eee0c07c0581d0826b02795492f72145bbfab3b0815096e
+MISC ChangeLog 526 RMD160 b9715fd25f0863a81b969d7624d67ca6dfc42ab6 SHA1 632cefe41a3dd212aa6debb7e87d93e2b2123417 SHA256 d562514892d95708dd06ee82f0150ffd124dd1540e423a94ad9bd0897867740a
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/blat/blat-33.ebuild b/sci-biology/blat/blat-33.ebuild
new file mode 100644
index 000000000..2c694aff1
--- /dev/null
+++ b/sci-biology/blat/blat-33.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit toolchain-funcs
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+LICENSE="blat"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+SRC_URI="http://www.soe.ucsc.edu/~kent/src/${PN}Src${PV}.zip"
+S="${WORKDIR}/${PN}Src"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+ MACHTYPE=$(tc-arch)
+ if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi
+ sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk"
+ mkdir -p "${S}/bin/${MACHTYPE}"
+ emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed"
+}
+
+src_install() {
+ MACHTYPE=$(tc-arch)
+ if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi
+ dobin "${S}/bin/${MACHTYPE}/"*
+}
diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild
new file mode 100644
index 000000000..665fdf9fe
--- /dev/null
+++ b/sci-biology/blat/blat-34.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit toolchain-funcs
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+LICENSE="blat"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+SRC_URI="http://www.soe.ucsc.edu/~kent/src/${PN}Src${PV}.zip"
+S="${WORKDIR}/${PN}Src"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+ MACHTYPE=$(tc-arch)
+ if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi
+ sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk"
+ sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk}
+ mkdir -p "${S}/bin/${MACHTYPE}"
+ emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed"
+}
+
+src_install() {
+ MACHTYPE=$(tc-arch)
+ if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi
+ dobin "${S}/bin/${MACHTYPE}/"*
+}
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/blat/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/blossoc/ChangeLog b/sci-biology/blossoc/ChangeLog
new file mode 100644
index 000000000..00ebd7d0b
--- /dev/null
+++ b/sci-biology/blossoc/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/blossoc
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blossoc-1.1.1.ebuild:
+ Mass import from sunrise
+
+ 15 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blossoc-1.1.1.ebuild,
+ +metadata.xml:
+ new package (bug 161063)
+
diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
new file mode 100644
index 000000000..cc7432878
--- /dev/null
+++ b/sci-biology/blossoc/Manifest
@@ -0,0 +1,4 @@
+DIST blossoc-1.1.1.tar.gz 615190 RMD160 7c867e69671354abc5affb80d5e879f8fd5c762a SHA1 f71b903b4ffc1dbe832cd19cf0c09da30222b285 SHA256 964ba436d55caa7bf64ba417d43ddd123589494648360074237df195c6fb2dd4
+EBUILD blossoc-1.1.1.ebuild 480 RMD160 b072f0dc8e79d87f2829b56f93cab3ed0026d0c5 SHA1 9e14db25306b54fbd08cac2c518baf32941cf1d4 SHA256 6615272b267a2b9a2ac519cd03e585659631b178d103674e4bd2f356b9dfafd0
+MISC ChangeLog 347 RMD160 43d9906fdb776920242d4975222a4c7bcccfc8bf SHA1 a2249d6182411f7b7de8edf46d116d7394a723cb SHA256 a8da1493f4ce8884496710c596945fdf3510dc1f098a4ef53a87c96247c198d0
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/blossoc/blossoc-1.1.1.ebuild b/sci-biology/blossoc/blossoc-1.1.1.ebuild
new file mode 100644
index 000000000..38c712866
--- /dev/null
+++ b/sci-biology/blossoc/blossoc-1.1.1.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A linkage disequilibrium association mapping tool"
+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/"
+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="sci-libs/gsl"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ emake install DESTDIR="${D}" || die "emake install failed"
+}
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/blossoc/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog
new file mode 100644
index 000000000..f21e33a49
--- /dev/null
+++ b/sci-biology/clover/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/clover
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +clover-2006.07.17.ebuild:
+ Mass import from sunrise
+
+ 15 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +clover-2006.07.17.ebuild,
+ +metadata.xml:
+ new package (bug 142269)
+
diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest
new file mode 100644
index 000000000..6b16e5c70
--- /dev/null
+++ b/sci-biology/clover/Manifest
@@ -0,0 +1,5 @@
+DIST clover-2006-07-17.tar.gz 15610 RMD160 e7f5c2b53afef2df292f9274b2a1ce2c1fbbc0c3 SHA1 f80b528ceb9833d0465b1196ae793c5364a87109 SHA256 e7b5b9fa8a341d49d9cf79a6d03ef0677a493f0c34a9a2f466a864575af91cb9
+DIST jaspar2005core 14913 RMD160 6fe43472cc1a2e0389ad9290801db56488773d3e SHA1 be8cdff62cf35f430c0c17f53564529b08000c9c SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4
+EBUILD clover-2006.07.17.ebuild 1059 RMD160 968519d9c6c17d29102ae9b6465acfe3812bcae7 SHA1 873e0f380eac7567ef3c2f9ee29fbc619a31fc4f SHA256 0ed8a75004280210ccd56dfb5c510bca400ece76cddbe3728ea3674f52387bd6
+MISC ChangeLog 356 RMD160 648c4b8a14af9917a83ef1bcbd8dff38ba42b957 SHA1 c9bde15410e08f200396143117e4ccd3becf7fe9 SHA256 41819363e8b5dcf8d67293fe33b7bd9c91f85acf983e1983b8b70f78a3d39bba
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/clover/clover-2006.07.17.ebuild b/sci-biology/clover/clover-2006.07.17.ebuild
new file mode 100644
index 000000000..4cf143b0f
--- /dev/null
+++ b/sci-biology/clover/clover-2006.07.17.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator toolchain-funcs
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs"
+HOMEPAGE="http://zlab.bu.edu/clover/"
+SRC_URI="http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz http://zlab.bu.edu/clover/jaspar2005core"
+
+LICENSE="as-is"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}-${MY_PV}"
+
+src_unpack() {
+ unpack ${PN}-${MY_PV}.tar.gz
+}
+
+src_compile() {
+ sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ dobin clover
+ dodir "/usr/share/${PN}"
+ insinto "/usr/share/${PN}"
+ doins ${DISTDIR}/jaspar2005core || die
+}
+
+pkg_postinst() {
+ einfo "The motif library jaspar2005core has been installed in"
+ einfo " /usr/share/clover/jaspar2005core"
+ einfo "You can pass this library to clover for motif search, or use your own library."
+}
diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/clover/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog
new file mode 100644
index 000000000..acdb0cf3c
--- /dev/null
+++ b/sci-biology/cluster/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/cluster
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 09 Aug 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+ Initial import of cluster-1.36 thanks to Favero Francesco
+
diff --git a/sci-biology/cluster/Manifest b/sci-biology/cluster/Manifest
new file mode 100644
index 000000000..6ecd70966
--- /dev/null
+++ b/sci-biology/cluster/Manifest
@@ -0,0 +1,5 @@
+AUX cluster-1.36-helpmenu-fix.patch 1287 RMD160 825d60b78925cc1c1d914bb0cea1a9953080f0c5 SHA1 45c42fe412ad428359f773e99382546ab2cfc2f9 SHA256 a90c835dd2d4a8196bffa67737c5755a5c5bed1be62772a76fcf0229ffaf47d4
+DIST cluster-1.36.tar.gz 971192 RMD160 72dea711c915074bca8d6186af285f8640bdfd43 SHA1 69bb0de8e5fb9d6bf5ab29b53d65b21ab97cc4ce SHA256 76f73740a2c8725e704780643cfac11875c957ba85254114946dccf3326caccf
+EBUILD cluster-1.36.ebuild 1552 RMD160 9fb48feb8d7075ca4bf5a99e4ecf6e5c72b1a08c SHA1 7de36808ea8504f6ae63b0e7b863237d9527a898 SHA256 1dc66ec426ff85419e4577936de52b43ca006b1c58e274e3b661340d41344ff0
+MISC ChangeLog 240 RMD160 c5b167761fa7fd0cb47ddbe0794f1851e367900f SHA1 6ea851b7d41fa95bb7dda862f416f9f9ed68acf8 SHA256 598dcd0f0044117a1049091c32988913dc7597b91cbc9b5ed715bb4d6d6d1c3e
+MISC metadata.xml 380 RMD160 a1c3ba6e6674088b1f06f1d8554b0457d5a95154 SHA1 eaf44b343cd9b336365d6a5858e41cf62dadd39b SHA256 4893d94442ec3c749ddb0fef6e62257e98b435e1709d4e71fc0f6c4ceea52dc2
diff --git a/sci-biology/cluster/cluster-1.36.ebuild b/sci-biology/cluster/cluster-1.36.ebuild
new file mode 100644
index 000000000..5af64c16b
--- /dev/null
+++ b/sci-biology/cluster/cluster-1.36.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+inherit autotools
+SRC_URI="${P}.tar.gz"
+
+DESCRIPTION="Clustering software for microarray analysis"
+HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X"
+
+DEPEND="X? ( virtual/motif )"
+RDEPEND="X? ( x11-misc/xdg-utils app-text/xpdf )"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
+}
+
+src_unpack() {
+ unpack "${A}"
+ cd "${S}"
+ sed -i \
+ -e 's:^docdir = $(prefix)/cluster/doc:docdir = @docdir@:' \
+ -e 's:^htmldir = $(prefix)/cluster/html:htmldir = @htmldir@:' \
+ -e 's:^imagedir = $(prefix)/cluster/html/images:imagedir = @htmldir@/images:' \
+ -e 's:^fileformatdir = $(prefix)/cluster:fileformatdir = @docdir@:' \
+ X11/Makefile.in || die "sed failed"
+
+ epatch "${FILESDIR}/${P}-helpmenu-fix.patch" || die "failed to patch helpmenu"
+
+}
+
+src_compile() {
+
+ econf $(use_with X x) \
+ --docdir="/usr/share/doc/${P}" \
+ --htmldir="/usr/share/doc/${P}/html" \
+ || die "econf failed"
+
+ emake || die "emake failed"
+}
+
+src_install() {
+ cd ${S}
+ emake DESTDIR="${D}" install || die "Install failed"
+
+ dodoc README COPYING AUTHORS ChangeLog NEWS TODO || die "failed to install docs"
+ insinto /usr/share/doc/${P}/examples
+ doins example/example.c example/README || die "failed to install docs"
+ insinto /usr/share/doc/${P}
+ doins doc/cluster.pdf || die "failed to install docs"
+
+}
diff --git a/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch
new file mode 100644
index 000000000..69f3a963e
--- /dev/null
+++ b/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch
@@ -0,0 +1,30 @@
+--- X11/gui.c 2007-05-05 00:21:30.000000000 -0500
++++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500
+@@ -1786,15 +1786,15 @@
+ { int item_no = (int) client_data;
+ switch (item_no)
+ { case CMD_HELP_HTMLHELP:
+- { system("netscape "PREFIX"/cluster/html/index.html &");
++ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &");
+ break;
+ }
+ case CMD_HELP_MANUAL:
+- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &");
++ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &");
+ break;
+ }
+ case CMD_HELP_DOWNLOAD:
+- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
++ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
+ break;
+ }
+ case CMD_HELP_FILEFORMAT:
+@@ -1852,7 +1852,7 @@
+ XtManageChild(widget);
+ free(helptext);
+ n = 0;
+- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0);
++ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0);
+ XtSetArg(args[n], XmNx, 10); n++;
+ XtSetArg(args[n], XmNy, 410); n++;
+ XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++;
diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml
new file mode 100644
index 000000000..2971c5ba0
--- /dev/null
+++ b/sci-biology/cluster/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+<email>je_fro@gentoo.org</email>
+<name>Jeff Gardner</name>
+</maintainer>
+<longdescription lang="en">
+Cluster provides an interface to access methods of gene expression data
+analysis.
+</longdescription>
+</pkgmetadata>
+
diff --git a/sci-biology/exonerate/ChangeLog b/sci-biology/exonerate/ChangeLog
new file mode 100644
index 000000000..1ffae2c7d
--- /dev/null
+++ b/sci-biology/exonerate/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/exonerate
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 18 Jan 2008; Jeff Gardner <je_fro@gentoo.org> +exonerate-1.4.0.ebuild:
+ Initial import thanks to dawe on bug #206521
+
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
new file mode 100644
index 000000000..a00ecb6f4
--- /dev/null
+++ b/sci-biology/exonerate/Manifest
@@ -0,0 +1,4 @@
+DIST exonerate-1.4.0.tar.gz 457837 RMD160 3239393bcc1e0a9c49c0f355aec1ff05e6824829 SHA1 6e4dca4fc0df9558f5bef8e5fef7244f8c72ae93 SHA256 adc47ca5192986c73bc3ba16e0bf4b176623f855a2a8598eab7093a77292a812
+EBUILD exonerate-1.4.0.ebuild 786 RMD160 7f5ffe4d60ebc952c4f43f656d783ccb3f48f845 SHA1 3e2b70693684e23a6c5f285b0dccd6c644fc591b SHA256 3eebf705180b5fcb761a50ff2d3eabbc7d5f3dfa5fe4d0db1215f1e1881d8f8c
+MISC ChangeLog 243 RMD160 1af40ad67df059c36978d712731d1bb53ee42947 SHA1 1802e86cc7e2f1b98baa60b913f9a17b63c1ad89 SHA256 a3eb147da81d6918ab71147efeda1bbb8094bfac274b45fb1b7616efca12a187
+MISC metadata.xml 359 RMD160 8002074ad4b87cad0d43249a73832926757fd686 SHA1 ff74d160352349027a6042e3e0abc6b26207582a SHA256 9427f7c3f59307e33e7708986d8127df195293c09d77f0a0c4cdb2ba5d255df8
diff --git a/sci-biology/exonerate/exonerate-1.4.0.ebuild b/sci-biology/exonerate/exonerate-1.4.0.ebuild
new file mode 100644
index 000000000..3b64c3c21
--- /dev/null
+++ b/sci-biology/exonerate/exonerate-1.4.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="exonerate is a generic tool for pairwise sequence comparison"
+HOMEPAGE="http://www.ebi.ac.uk/~guy/exonerate/"
+SRC_URI="http://www.ebi.ac.uk/~guy/exonerate/${P}.tar.gz"
+
+LICENSE="LGPL"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="largefile utils"
+
+DEPEND="dev-libs/glib"
+RDEPEND=""
+
+src_compile() {
+
+ local myconf=""
+
+ if has_version ">=dev-libs/glib-2.0"; then
+ myconf="${myconf} --enable-glib2"
+ fi
+
+ econf \
+ $( use_enable largefile ) \
+ $( use_enable utils utilities ) \
+ ${myconf} \
+ || die "econf failed"
+
+ emake -j1 || die "emake failed"
+}
+
+src_install() {
+
+ emake DESTDIR="${D}" install || die "Install failed"
+ doman doc/man/man1/*.1
+ dodoc README
+}
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
new file mode 100644
index 000000000..2721592ea
--- /dev/null
+++ b/sci-biology/exonerate/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+<email>je_fro@gentoo.org</email>
+<name>Jeff Gardner</name>
+</maintainer>
+<longdescription lang="en">
+exonerate is a generic tool for pairwise sequence comparison
+</longdescription>
+</pkgmetadata>
+
diff --git a/sci-biology/generecon/ChangeLog b/sci-biology/generecon/ChangeLog
new file mode 100644
index 000000000..ff5a98428
--- /dev/null
+++ b/sci-biology/generecon/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/generecon
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*generecon-1.2.1 (19 Apr 2006)
+
+ 19 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com>:
+ +generecon-1.2.1.ebuild, +metadata.xml, +ChangeLog,
+ Initial import. Thanks to Neil <nshephard@gmail.com>
+ for the initial ebuild. Closes bug #128514.
diff --git a/sci-biology/generecon/Manifest b/sci-biology/generecon/Manifest
new file mode 100644
index 000000000..9157588f1
--- /dev/null
+++ b/sci-biology/generecon/Manifest
@@ -0,0 +1,5 @@
+AUX generecon-docfiles.patch 435 RMD160 ce732399b02f42a0089ea82ea240098dfb8207c5 SHA1 4f6ed16b9ce8f118b99a47d9e36ffa304e42e8bb SHA256 37fbf94d6716a489e6a59f119cf617b9ff024e612dc96323d2297f9c09360175
+DIST generecon-1.2.1.tar.gz 238270 RMD160 f625ec81db88556a33e76f63c5c242b70e951f0f SHA1 a1562a21eab88d6ac1b2d2c046b87414ff703d4b SHA256 b35496ab6baf0bda45dc7a934385441cc92bfac39cb0a261a541ad8b258ba446
+EBUILD generecon-1.2.1-r1.ebuild 1017 RMD160 74ae5fc49e83237421fdcd81270a393e3657107b SHA1 d8ee9592d814f78d4751bb7a32e69bbd2c545815 SHA256 7ba69a4147c5feac1f03a63e5db6c7fa6d0dec342681f45b10b437874588b396
+MISC ChangeLog 363 RMD160 19d0d4926d34d52c906e11fef60b3d7d713c0b4f SHA1 d3248b7ba9d5b2aa8af1c6c77802199041720c0e SHA256 9a3bb08c6357408656ecf892cbe5e25eb62f53211e8276237b383d7548755242
+MISC metadata.xml 261 RMD160 d7630eceb5ae049fa36c58ed3c9f6fe7780c15bf SHA1 6ded05d9eaded2a6b810b7f80dd2dc3270bbff8e SHA256 8bbae243cac9cf6fc1d24a0582390bd1184df161f4d7f87300874e6a7860b15c
diff --git a/sci-biology/generecon/files/generecon-docfiles.patch b/sci-biology/generecon/files/generecon-docfiles.patch
new file mode 100644
index 000000000..79d63e73f
--- /dev/null
+++ b/sci-biology/generecon/files/generecon-docfiles.patch
@@ -0,0 +1,12 @@
+diff -Nuar generecon-1.2.1.orig/Makefile.am generecon-1.2.1/Makefile.am
+--- generecon-1.2.1.orig/Makefile.am 2006-04-19 12:52:18.000000000 -0300
++++ generecon-1.2.1/Makefile.am 2006-04-19 12:55:53.000000000 -0300
+@@ -31,7 +31,7 @@
+ bin_PROGRAMS = generecon
+
+
+-docdir = ${prefix}/share/generecon/doc
++docdir = ${prefix}/share/doc/#PF#
+ dist_doc_DATA =
+ test_inputdir = ${prefix}/share/generecon/test-input
+ dist_test_input_DATA =
diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
new file mode 100644
index 000000000..7adfb5cf5
--- /dev/null
+++ b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils
+
+DESCRIPTION="Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods."
+HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/"
+SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz"
+SLOT="0"
+
+# License of the package. This must match the name of file(s) in
+# /usr/portage/licenses/. For complex license combination see the developer
+# docs on gentoo.org for details.
+LICENSE="GPL-2"
+
+KEYWORDS="x86"
+
+DEPEND="dev-scheme/guile
+ sci-libs/gsl"
+
+src_unpack() {
+ unpack ${A}
+ sed 's|#PF#|'${PF}'|g' ${FILESDIR}/${PN}-docfiles.patch > ${PN}-docfiles.patch
+
+ epatch ${PN}-docfiles.patch
+
+ cd ${S}
+ pwd
+ einfo "Regenerating autotools files..."
+ aclocal || die "aclocal failed"
+ automake || die "automake failed"
+}
+
+src_install() {
+ make DESTDIR=${D} install || die "make install failed"
+}
diff --git a/sci-biology/generecon/metadata.xml b/sci-biology/generecon/metadata.xml
new file mode 100644
index 000000000..963198591
--- /dev/null
+++ b/sci-biology/generecon/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <maintainer>
+ <email>lucas.chiesa@gmail.com</email>
+ <name>Lucas Chiesa</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/generic-genome-browser/ChangeLog b/sci-biology/generic-genome-browser/ChangeLog
new file mode 100644
index 000000000..c23f8b8cc
--- /dev/null
+++ b/sci-biology/generic-genome-browser/ChangeLog
@@ -0,0 +1,51 @@
+# ChangeLog for sci-biology/generic-genome-browser
+# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+
+ 29 Jul 2007; Christian Heim <phreak@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ Fixing the DEPEND/RDEPEND for the move of net-www/apache to
+ www-servers/apache (#78622).
+
+ 23 Nov 2006; Francesco Riosa <vivo@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ dev-db/mysql => virtual/mysql
+
+ 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+ Stepping down from maintaining this package.
+
+ 13 Feb 2006; Michael Cummings <mcummings@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ Virtuals for some perl-core deps
+
+ 28 Nov 2005; <mcumming@gentoo.org> generic-genome-browser-1.58.ebuild:
+ Switched from perl-module to perl-app eclass
+
+ 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+ Maintainer changed from Stephen Diener (MIA) to Olivier Fisette.
+
+ 24 May 2005; Michael Cummings <mcummings@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ dev-perl/Digest-MD5 => perl-core/Digest-MD5
+
+ 24 May 2005; Michael Cummings <mcummings@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ dev-perl/CGI => perl-core/CGI
+
+*generic-genome-browser-1.58 (23 Dec 2004)
+
+ 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+ +generic-genome-browser-1.58.ebuild:
+ Moved from app-sci/generic-genome-browser to
+ sci-biology/generic-genome-browser.
+
+ 03 Aug 2004; David Holm <dholm@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ Added to ~ppc.
+
+*generic-genome-browser-1.58 (13 Jan 2004)
+
+ 13 Jan 2004; Stephen Diener <sediener@gentoo.org>
+ generic-genome-browser-1.58.ebuild:
+ Initial import
+
diff --git a/sci-biology/generic-genome-browser/Manifest b/sci-biology/generic-genome-browser/Manifest
new file mode 100644
index 000000000..8dcab2cc1
--- /dev/null
+++ b/sci-biology/generic-genome-browser/Manifest
@@ -0,0 +1,4 @@
+DIST Generic-Genome-Browser--1.68.tar.gz 2145950 RMD160 093df1e5e170e7fa33c63865ca54ea90b9f0d4fd SHA1 487b8453f722c63ada9c62a4190235be6684897b SHA256 5b5ed7f504a9646d158f0a99d37c0e2b45e3d602b140a5eac261c92478c4ae6b
+EBUILD generic-genome-browser-1.68.ebuild 2284 RMD160 fded262e1cbe15982c38fb473acf6dfe16f15df3 SHA1 03ed326d6023126ac0bfdb70215f4f688e1be099 SHA256 212598ace888fa337c7931b414d0c7291741c36fc25c3e67e0a96eb184bd58a8
+MISC ChangeLog 1800 RMD160 945635f595dee6335828affd4d042c173e570cf3 SHA1 419375011a04db77048ac39dfdaffc613dfdcb86 SHA256 a59e36913cf1616e2e125dfa1a5e0f2c5140a61e3701bf0e80107298053f5f9d
+MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
diff --git a/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild b/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild
new file mode 100644
index 000000000..45ee5b82f
--- /dev/null
+++ b/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $
+
+inherit perl-app
+
+MY_PN="Generic-Genome-Browser"
+
+# I don't know if the '--' is a typo... TODO contact somebody and find out.
+MY_P="${MY_PN}--${PV}"
+
+DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
+HOMEPAGE="http://www.gmod.org"
+SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~x86 ~ppc ~amd64"
+IUSE="mysql gd"
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+DEPEND="
+ >=sci-biology/bioperl-1.4
+ >=virtual/perl-CGI-2.56
+ >=dev-perl/GD-2.07
+ dev-perl/DBI
+ virtual/perl-Digest-MD5
+ dev-perl/Text-Shellwords
+ dev-perl/libwww-perl
+ dev-perl/XML-Parser
+ dev-perl/XML-Writer
+ dev-perl/XML-Twig
+ dev-perl/XML-DOM
+ dev-perl/Bio-Das
+ gd? (
+ dev-perl/GD-SVG
+ )
+ mysql?
+ (
+ >=virtual/mysql-4.0
+ dev-perl/DBD-mysql
+ )
+ >=www-servers/apache-2.0.47"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+
+ cd ${S}
+# ewarn "Modifying Makefile.PL to avoid sandbox violation"
+ sed -e "s:WriteMakefile(:WriteMakefile(\n 'PREFIX'=>'${D}/usr',\n'INSTALLDIRS' => 'vendor',:" -i Makefile.PL \
+ || die "Failed to sed Makefile.PL"
+
+ perl Makefile.PL \
+ HTDOCS=/var/www/localhost/htdocs \
+ CGIBIN=/var/www/localhost/cgi-bin \
+ CONF=/etc \
+ PREFIX=/var/www/localhost \
+ DESTDIR=${D} \
+ INSTALLDIRS=vendor
+ #perl-module_src_compile || die "Make failed"
+ perl-module_src_test || die "Test Failed"
+}
+
+# Might want to look at how to use webapp with this.
+
+src_install() {
+ dodir /etc
+ dodir /var/www/localhost/htdocs
+ dodir /var/www/localhost/cgi-bin
+ mydoc="History README TODO INSTALL"
+ dodir /usr/share/${PF}/tutorial
+ cd ${S}/docs/tutorial
+ tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+ cd ${S}
+ sed -e "s:my \$dir = \":my \$dir = \"${D}/:" -i install_util/conf_install.PLS || die "sed1 failed"
+ sed -e "s:my \$ht_target = \":my \$ht_target = \"${D}/:" -i install_util/htdocs_install.PLS || die "sed2 failed"
+ sed -e "s:my \$cgi_target = :my \$cgi_target = \"${D}\"\.:" -i install_util/cgi_install.PLS || die "sed3 failed"
+
+ perl-module_src_install
+}
diff --git a/sci-biology/generic-genome-browser/metadata.xml b/sci-biology/generic-genome-browser/metadata.xml
new file mode 100644
index 000000000..d4648212c
--- /dev/null
+++ b/sci-biology/generic-genome-browser/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
new file mode 100644
index 000000000..2fc95e1e1
--- /dev/null
+++ b/sci-biology/glimmer/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/glimmer
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmer-3.02.ebuild:
+ Mass import from sunrise
+
+ 14 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmer-3.02.ebuild,
+ +metadata.xml:
+ new package sci-biology/glimmer (bug 170895)
+
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
new file mode 100644
index 000000000..055635a18
--- /dev/null
+++ b/sci-biology/glimmer/Manifest
@@ -0,0 +1,4 @@
+DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221
+EBUILD glimmer-3.02.ebuild 839 RMD160 5f3881415516349d932ea51632b8ae19f5e3c0af SHA1 979d34e653b1139a6400f694161133634d40ec69 SHA256 00f660e15cfe8084b3b65e488e5041743194722b7786ca114f22ec368b6e11e5
+MISC ChangeLog 365 RMD160 07fd0d884f3aebb2fc0c13de4d3f0df1d391ca85 SHA1 14ae9ea74f773515a0109a3c223a685e2c488cd3 SHA256 88f2c93b45b8e227684111cd0c2780229cc20937826784e70156b3146749a161
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/glimmer/glimmer-3.02.ebuild b/sci-biology/glimmer/glimmer-3.02.ebuild
new file mode 100644
index 000000000..2814ad994
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(delete_all_version_separators)
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${PN}${PV}
+
+src_compile() {
+ sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
+ cd src
+ emake || die "emake failed"
+}
+
+src_install() {
+ rm bin/test
+ dobin bin/*
+
+ dodir /usr/share/${PN}/scripts
+ insinto /usr/share/${PN}/scripts
+ doins scripts/*
+
+ dodoc glim302notes.pdf
+}
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/glimmer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog
new file mode 100644
index 000000000..918e4112f
--- /dev/null
+++ b/sci-biology/glimmerhmm/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-biology/glimmerhmm
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +glimmerhmm-3.0.1.ebuild:
+ Mass import from sunrise
+
+ 15 Mar 2007; Christian Faulhammer <opfer@gentoo.org>
+ glimmerhmm-3.0.1.ebuild:
+ Orthographic sex-up
+
+ 14 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmerhmm-3.0.1.ebuild,
+ +metadata.xml:
+ new package sci-biology/glimmerhmm (bug 170964)
+
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
new file mode 100644
index 000000000..75fec2457
--- /dev/null
+++ b/sci-biology/glimmerhmm/Manifest
@@ -0,0 +1,4 @@
+DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4
+EBUILD glimmerhmm-3.0.1.ebuild 1256 RMD160 63bbac5df129a0867aa0ab6e025710c8683cdcf6 SHA1 c517e20085e5e716435c0d29bd1a3bae9228e2d1 SHA256 0a9df33ae04c5b275999041573f0935b32be4797da0b48211e88dbe277d7dfe5
+MISC ChangeLog 486 RMD160 7d213d91b90390472c3afbf1a921ccbbfc6111c3 SHA1 7c1d8b78c09b3c2344874ca9923aab99cf0656d8 SHA256 87dcfa56bc3f3a8f104c7fcf893596d6ab677a982af26651336a7b8854fd31f1
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
new file mode 100644
index 000000000..61f3a2740
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="An eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${MY_P}
+
+src_compile() {
+ sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \
+ -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' train/trainGlimmerHMM || die "sed failed"
+ sed -i 's/^CFLAGS[ ]*=.*//' */makefile
+
+ cd sources
+ emake || die "emake failed in sources"
+ cd "${S}/train" || die "failed to cd"
+ emake || die "emake failed in train"
+}
+
+src_install() {
+ dobin sources/glimmerhmm train/trainGlimmerHMM
+
+ dodir /usr/share/${PN}/{lib,models,training_utils}
+ insinto /usr/share/${PN}/lib
+ doins train/*.pm
+ insinto /usr/share/${PN}/models
+ doins -r trained_dir/*
+ insinto /usr/share/${PN}/training_utils
+ insopts -m755
+ doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+ dodoc README.first train/readme.train
+}
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/glimmerhmm/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/gmap/ChangeLog b/sci-biology/gmap/ChangeLog
new file mode 100644
index 000000000..6e87b45e7
--- /dev/null
+++ b/sci-biology/gmap/ChangeLog
@@ -0,0 +1,31 @@
+# ChangeLog for sci-biology/gmap
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 11 Sep 2007; weaver <weaver@horizon.ath.cx> +gmap-2007.07.16.ebuild:
+ version bump
+
+ 30 May 2007; weaver <weaver@horizon.ath.cx> files/digest-gmap-2007.05.25,
+ Manifest:
+ upstream re-rolled tarball due to single bug, updating digests
+
+ 29 May 2007; weaver <weaver@horizon.ath.cx> +gmap-2007.05.25.ebuild:
+ version bump
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> ChangeLog:
+ Mass import from sunrise
+
+ 15 Apr 2007; Stefan Schweizer <genstef@gentoo.org> gmap-2006.12.18.ebuild:
+ Remove RESTRICT=mirror, gmap license allows redistribution
+
+ 09 Jan 2007; Markus Ullmann <jokey@gentoo.org> -gmap-2006.12.12.ebuild:
+ Drop old
+
+ 03 Jan 2007; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx>
+ +gmap-2006.12.18.ebuild:
+ new version
+
+ 12 Dec 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx>
+ +gmap-20060421.ebuild, +metadata.xml:
+ New ebuild, see Bug 135103
+
diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest
new file mode 100644
index 000000000..8251fe2f3
--- /dev/null
+++ b/sci-biology/gmap/Manifest
@@ -0,0 +1,8 @@
+DIST gmap-2006-12-18.tar.gz 829170 RMD160 fb247cc2c792ebb49742b33eecec2352b75c5123 SHA1 d9f2f7248176897c153f15bc00029a703fed6c5a SHA256 992f9f2058f83b4a84ffb84c9aaba75fc18d8ccdb0a0be66086f7f94f3ba5675
+DIST gmap-2007-05-25.tar.gz 953535 RMD160 203ae638492522e9acea435b1128386b19185ec1 SHA1 c167fc0d50816caae5e964464bcb60abd6087e8d SHA256 f1488314856819940ca39f4f7f106e2099e43d29d7e95e047cee7771357ce506
+DIST gmap-2007-07-16.tar.gz 964986 RMD160 ea375b06eb6d14c0c4d2b2d07374f81792b81ccd SHA1 6862cd16b156720f374a967be6b9dc9f71878bc5 SHA256 9634bde9f2a59630561eee957bd2fc90a96e20d1859ca00180a16279ad8e40f1
+EBUILD gmap-2006.12.18.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54
+EBUILD gmap-2007.05.25.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54
+EBUILD gmap-2007.07.16.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54
+MISC ChangeLog 1001 RMD160 5d1a59e49fe0f3048cdb9813d69678d81865c9cd SHA1 e9db8a958d3b2cfcfcf052884f14f6de154ad806 SHA256 922b20dc231bf2032749dd92237c7a0d644d5411d154770f89ff3e5271747b33
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/gmap/gmap-2006.12.18.ebuild b/sci-biology/gmap/gmap-2006.12.18.ebuild
new file mode 100644
index 000000000..2ee4ed983
--- /dev/null
+++ b/sci-biology/gmap/gmap-2006.12.18.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://www.gene.com/share/gmap/"
+SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/gmap-${MY_PV}"
+
+src_install() {
+ emake install DESTDIR="${D}" || die "emake install failed"
+ dodoc AUTHORS ChangeLog README
+}
diff --git a/sci-biology/gmap/gmap-2007.05.25.ebuild b/sci-biology/gmap/gmap-2007.05.25.ebuild
new file mode 100644
index 000000000..2ee4ed983
--- /dev/null
+++ b/sci-biology/gmap/gmap-2007.05.25.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://www.gene.com/share/gmap/"
+SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/gmap-${MY_PV}"
+
+src_install() {
+ emake install DESTDIR="${D}" || die "emake install failed"
+ dodoc AUTHORS ChangeLog README
+}
diff --git a/sci-biology/gmap/gmap-2007.07.16.ebuild b/sci-biology/gmap/gmap-2007.07.16.ebuild
new file mode 100644
index 000000000..2ee4ed983
--- /dev/null
+++ b/sci-biology/gmap/gmap-2007.07.16.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://www.gene.com/share/gmap/"
+SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/gmap-${MY_PV}"
+
+src_install() {
+ emake install DESTDIR="${D}" || die "emake install failed"
+ dodoc AUTHORS ChangeLog README
+}
diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/gmap/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/kalign/ChangeLog b/sci-biology/kalign/ChangeLog
new file mode 100644
index 000000000..67a193de8
--- /dev/null
+++ b/sci-biology/kalign/ChangeLog
@@ -0,0 +1,14 @@
+# ChangeLog for sci-biology/kalign
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 29 Apr 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+ Added ~amd64.
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +kalign-2.03.ebuild:
+ Mass import from sunrise
+
+ 18 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +kalign-2.03.ebuild,
+ +metadata.xml:
+ New Ebuild for bug 175116
+
diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest
new file mode 100644
index 000000000..c3e71af19
--- /dev/null
+++ b/sci-biology/kalign/Manifest
@@ -0,0 +1,4 @@
+DIST kalign_2.03.orig.tar.gz 114022 RMD160 e4677db9983b4bf567515c535dbd1f61cfdd70bd SHA1 c856d14b537a9139fc601e4de98870293a3aceb4 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0
+EBUILD kalign-2.03.ebuild 536 RMD160 2cc4f600154760ca29b3c41fffeed128f8a0a801 SHA1 4433b0feb1c6720c4dfff08fcc97bccf24118c06 SHA256 52d45d11ba9e5f90ca12de2927fb5db26f4b5fcb0e28019fb86d31c01351de5f
+MISC ChangeLog 419 RMD160 72d69f8332f99e4b58a46707558bff19b59dd8e6 SHA1 4d72254308497640ffe39ef4697e263cb46b172a SHA256 0735f0f319d06c45cea72529a5c6f0e099a68ba2653852af4e89c0ec2bb34c4a
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/kalign/kalign-2.03.ebuild b/sci-biology/kalign/kalign-2.03.ebuild
new file mode 100644
index 000000000..79bea1903
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+ unpack ${A}
+ sed -i 's/^CFLAGS.*= -O9/CFLAGS := ${CFLAGS} -O3/' ${S}/Makefile.in
+}
+
+src_install() {
+ dobin kalign
+ dodoc README
+}
diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/kalign/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog
new file mode 100644
index 000000000..b0bc8509d
--- /dev/null
+++ b/sci-biology/mummer/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/mummer
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +mummer-3.19.ebuild:
+ Mass import from sunrise
+
+ 07 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +mummer-3.19.ebuild,
+ +metadata.xml:
+ New package, Bug 169793
+
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
new file mode 100644
index 000000000..e439ca264
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,4 @@
+DIST MUMmer3.19.tar.gz 3141991 RMD160 54f3c692efb8bde7762c48186919754f2a8c178c SHA1 8906bab6bd43b307461de8b5f44122a115799533 SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab
+EBUILD mummer-3.19.ebuild 1462 RMD160 5f8b0b879579bbb191e127ff8502cf85ad24a1d6 SHA1 4fe7b3203592abf4fef23576225389304983102a SHA256 a4b07705f9363862d0a22418b3afbf90a1170653b3417f6217d69febf0ea70a5
+MISC ChangeLog 341 RMD160 3af940375849fd821b9a26f495ec4dfe0d0e43d2 SHA1 343e404673256e84eaa87aab34f23c2fd0e10677 SHA256 fba592d098848186f7e54967015b44ca01753a11251c505add0bd83d361364eb
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/mummer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.19.ebuild b/sci-biology/mummer/mummer-3.19.ebuild
new file mode 100644
index 000000000..a6b3e4c0c
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.19.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+MY_P=MUMmer${PV}
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${MY_P}
+
+src_compile() {
+ emake || die "emake failed"
+
+ sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ -e 's|\(set bindir = \).*|\1/usr/bin|' \
+ -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+ -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
+ sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+ dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+ exact-tandems promer repeat-match show-aligns gaps mummer \
+ show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/*
+ newbin annotate mummer-annotate
+
+ dodir /usr/share/${PN}/{lib,scripts}
+ insinto /usr/share/${PN}/scripts
+ doins scripts/{*.awk,*.csh,*.pl}
+ insinto /usr/share/${PN}/lib
+ doins scripts/Foundation.pm
+
+ dodoc ACKNOWLEDGEMENTS ChangeLog README
+ insinto /usr/share/doc/${PF}
+ use doc && doins -r docs
+}
diff --git a/sci-biology/perlprimer/Manifest b/sci-biology/perlprimer/Manifest
new file mode 100644
index 000000000..b77a0503b
--- /dev/null
+++ b/sci-biology/perlprimer/Manifest
@@ -0,0 +1,3 @@
+AUX gcg.801 56574 RMD160 b809e096c4709e9ee89e3f2d1b91906996668c95 SHA1 3962f4c111b7f30406e99afadc87c885b9fd125c SHA256 6b0541d33650e3ca02d5b957a7632d6d5a9f4b779188743c34fbb75283daaac3
+DIST perlprimer-1.1.14.tar.bz2 359485 RMD160 57f1ebc1476acb4a75e01268715c86919d92c3e7 SHA1 d62e76ffada5eddbf162fd0730c99d191d5de190 SHA256 8bac821a2711547c5bf68cfb58a61cc1b5d37a86b38a5db4313c46ddc05e3dfa
+EBUILD perlprimer-1.1.14.ebuild 942 RMD160 392288721f86e02941fae981d762863b09e5dc74 SHA1 1b6466f3cab1f6bfd07b2f93580d0b833daf306f SHA256 a8c7fcd50220dc5c23d3a1ad80f5528f98007db915b76d560f40fca47963f20a
diff --git a/sci-biology/perlprimer/files/gcg.801 b/sci-biology/perlprimer/files/gcg.801
new file mode 100644
index 000000000..53db0b7ad
--- /dev/null
+++ b/sci-biology/perlprimer/files/gcg.801
@@ -0,0 +1,769 @@
+
+REBASE version 801 gcg.801
+
+ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+ REBASE, The Restriction Enzyme Database http://rebase.neb.com
+ Copyright (c) Dr. Richard J. Roberts, 2008. All rights reserved.
+ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+
+Rich Roberts Dec 31 2007
+
+
+REBASE codes for commercial sources of enzymes
+
+ A GE Healthcare (8/05)
+ B Invitrogen Corporation (8/05)
+ C Minotech Biotechnology (12/07)
+ E Stratagene (9/05)
+ F Fermentas International Inc. (12/07)
+ G Qbiogene (12/07)
+ H American Allied Biochemical, Inc. (12/07)
+ I SibEnzyme Ltd. (12/07)
+ J Nippon Gene Co., Ltd. (12/07)
+ K Takara Bio Inc. (12/07)
+ M Roche Applied Science (12/07)
+ N New England Biolabs (12/07)
+ O Toyobo Biochemicals (12/07)
+ Q Molecular Biology Resources - CHIMERx (12/07)
+ R Promega Corporation (9/05)
+ S Sigma Chemical Corporation (9/05)
+ U Bangalore Genei (12/07)
+ V Vivantis Technologies (12/07)
+ W MP Biomedicals (12/07)
+ X EURx Ltd. (12/07)
+ Y CinnaGen Inc. (12/07)
+
+..
+AarI 11 CACCTGCnnnn'nnnn_ 4 ! >F
+;AasI 7 GACnn_nn'nnGTC -2 ! DrdI,DseDI >F
+;AatI 3 AGG'CCT 0 ! StuI,Eco147I,PceI,SseBI >O
+AatII 5 G_ACGT'C -4 ! ZraI >AFGIKMNORV
+AbsI 2 CC'TCGA_GG 4 ! >I
+AccI 2 GT'mk_AC 2 ! FblI,XmiI >ABGJKMNORSUWX
+;AccII 2 CG'CG 0 ! Bsh1236I,BspFNI,BstFNI,BstUI,MvnI >AJK
+;AccIII 1 T'CCGG_A 4 ! Aor13HI,BseAI,Bsp13I,BspEI,Kpn2I,MroI >GJKRW
+;Acc16I 3 TGC'GCA 0 ! AviII,FspI,NsbI >IV
+;Acc36I 10 ACCTGCnnnn'nnnn_ 4 ! BspMI,BfuAI,BveI >I
+Acc65I 1 G'GTAC_C 4 ! KpnI,Asp718I >FGINRVW
+;AccB1I 1 G'GyrC_C 4 ! BanI,BshNI,BspT107I >IV
+;AccB7I 7 CCAn_nnn'nTGG -3 ! PflMI,BasI,Van91I >IRV
+;AccBSI 3 CCG'CTC 0 ! BsrBI,MbiI >IV
+;AceIII 13 CAGCTCnnnnnnn'nnnn_ 4 ! >
+AciI 1 C'CG_C 2 ! BspACI,SsiI >N
+AclI 2 AA'CG_TT 2 ! Psp1406I >INV
+;AclWI 9 GGATCnnnn'n_ 1 ! AlwI,BspPI >I
+;AcoI 1 y'GGCC_r 4 ! CfrI,EaeI >I
+;AcsI 1 r'AATT_y 4 ! ApoI,XapI >IMV
+AcuI 22 CTGAAGnnnnnnnnnnnnnn_nn' -2 ! Eco57I >IN
+;AcvI 3 CAC'GTG 0 ! PmaCI,BbrPI,Eco72I,PmlI,PspCI >QX
+;AcyI 2 Gr'CG_yC 2 ! BsaHI,BssNI,BstACI,Hin1I,Hsp92I >JM
+;AdeI 6 CAC_nnn'GTG -3 ! DraIII >F
+;AfaI 2 GT'AC 0 ! RsaI,Csp6I,CviQI,RsaNI >AK
+AfeI 3 AGC'GCT 0 ! Eco47III,Aor51HI >IN
+;AfiI 7 CCnn_nnn'nnGG -3 ! BsiYI,Bsc4I,BseLI,BslI >V
+AflII 1 C'TTAA_G 4 ! BfrI,BspTI,Bst98I,MspCI,Vha464I >AJKNO
+AflIII 1 A'CryG_T 4 ! >GMNSW
+AgeI 1 A'CCGG_T 4 ! AsiGI,BshTI,CspAI,PinAI >JNR
+;AhaIII 3 TTT'AAA 0 ! DraI >
+AhdI 6 GACnn_n'nnGTC -1 ! Eam1105I,AspEI,BmeRI,DriI,EclHKI >N
+;AhlI 1 A'CTAG_T 4 ! SpeI,BcuI >IV
+;AjiI 3 CAC'GTC 0 ! BtrI,BmgBI >F
+;AjnI 0 'CCwGG_ 5 ! EcoRII,BseBI,BstNI,BstOI,Bst2UI,MvaI,Psp6I,PspGI >I
+AjuI 25 GAAnnnnnnnTTGGnnnnnn_nnnnn' -5 ! >F
+AjuI 26 CCAAnnnnnnnTTCnnnnnnn_nnnnn' -5 ! >F
+AleI 5 CACnn'nnGTG 0 ! OliI >N
+AlfI 24 GCAnnnnnnTGCnnnnnnnnnn_nn' -2 ! >F
+AloI 25 GAACnnnnnnTCCnnnnnnn_nnnnn' -5 ! >F
+AloI 25 GGAnnnnnnGTTCnnnnnnn_nnnnn' -5 ! >F
+AluI 2 AG'CT 0 ! AluBI >ABFGHIJKMNOQRSUVWXY
+;AluBI 2 AG'CT 0 ! AluI >I
+AlwI 9 GGATCnnnn'n_ 1 ! AclWI,BspPI >N
+;Alw21I 5 G_wGCw'C -4 ! Bbv12I,BsiHKAI >F
+;Alw26I 6 GTCTCn'nnnn_ 4 ! BsmAI,BstMAI >FR
+;Alw44I 1 G'TGCA_C 4 ! ApaLI,VneI >FJMORS
+;AlwFI 6 GAAAynnnnnrTG 0 ? ! >
+AlwNI 6 CAG_nnn'CTG -3 ! CaiI >N
+;Ama87I 1 C'yCGr_G 4 ! AvaI,BmeT110I,BsiHKCI,BsoBI,Eco88I >IV
+;Aor13HI 1 T'CCGG_A 4 ! AccIII,BseAI,Bsp13I,BspEI,Kpn2I,MroI >K
+;Aor51HI 3 AGC'GCT 0 ! Eco47III,AfeI >AK
+ApaI 5 G_GGCC'C -4 ! Bsp120I,PspOMI >ABFGIJKMNOQRSUVWX
+;ApaBI 8 GCA_nnnnn'TGC -5 ! BstAPI >
+ApaLI 1 G'TGCA_C 4 ! Alw44I,VneI >AKNU
+;ApeKI 1 G'CwG_C 3 ! TseI >N
+ApoI 1 r'AATT_y 4 ! AcsI,XapI >N
+AscI 2 GG'CGCG_CC 4 ! PalAI,SgsI >GNW
+AseI 2 AT'TA_AT 2 ! VspI,PshBI >JNO
+;AsiGI 1 A'CCGG_T 4 ! AgeI,BshTI,CspAI,PinAI >IV
+AsiSI 5 GCG_AT'CGC -2 ! SgfI,RgaI >N
+;AspI 4 GACn'n_nGTC 1 ! Tth111I,PflFI,PsyI >M
+;Asp700I 5 GAAnn'nnTTC 0 ! XmnI,MroXI,PdmI >M
+;Asp718I 1 G'GTAC_C 4 ! KpnI,Acc65I >M
+;AspA2I 1 C'CTAG_G 4 ! AvrII,BlnI,XmaJI >IV
+;AspCNI 2 GCCGC 0 ? ! >
+;AspEI 6 GACnn_n'nnGTC -1 ! Eam1105I,AhdI,BmeRI,DriI,EclHKI >M
+;AspLEI 3 G_CG'C -2 ! HhaI,BstHHI,CfoI,Hin6I,HinP1I,HspAI >IV
+;AspS9I 1 G'GnC_C 3 ! BmgT120I,Cfr13I,Sau96I >IV
+;AssI 3 AGT'ACT 0 ! ScaI,BmcAI,ZrmI >U
+;AsuI 1 G'GnC_C 3 ! AspS9I,BmgT120I,Cfr13I,Sau96I >
+;AsuII 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BspT104I,BstBI,Csp45I,NspV,SfuI >
+;AsuC2I 2 CC's_GG 1 ! BcnI,BpuMI,NciI >I
+;AsuHPI 13 GGTGAnnnnnnn_n' -1 ! HphI >IV
+;AsuNHI 1 G'CTAG_C 4 ! NheI,BmtI,BspOI >IV
+AvaI 1 C'yCGr_G 4 ! Ama87I,BmeT110I,BsiHKCI,BsoBI,Eco88I >ABGJMNORSUWX
+AvaII 1 G'GwC_C 3 ! Bme18I,Eco47I,SinI,VpaK11BI >AGJKMNRSWY
+;AvaIII 3 ATGCAT 0 ? ! EcoT22I,Mph1103I,NsiI,Zsp2I >
+;AviII 3 TGC'GCA 0 ! Acc16I,FspI,NsbI >M
+AvrII 1 C'CTAG_G 4 ! AspA2I,BlnI,XmaJI >N
+;AxyI 2 CC'TnA_GG 3 ! Bse21I,Bsu36I,Eco81I >J
+BaeI 23 ACnnnnGTAyCnnnnnnn_nnnnn' -5 ! >N
+BaeI 26 GrTACnnnnGTnnnnnnnnnn_nnnnn' -5 ! >N
+;BalI 3 TGG'CCA 0 ! MlsI,MluNI,MscI,Msp20I >AJKR
+BamHI 1 G'GATC_C 4 ! >ABFGHIJKMNOQRSUVWXY
+BanI 1 G'GyrC_C 4 ! AccB1I,BshNI,BspT107I >NORU
+BanII 5 G_rGCy'C -4 ! Eco24I,EcoT38I,FriOI >AGKMNOQRSWX
+;BanIII 2 AT'CG_AT 2 ! ClaI,Bsa29I,BseCI,BshVI,BspDI,BspXI,Bsu15I,BsuTUI >O
+BarI 25 GAAGnnnnnnTACnnnnnnn_nnnnn' -5 ! >I
+BarI 25 GTAnnnnnnCTTCnnnnnnn_nnnnn' -5 ! >I
+;BasI 7 CCAn_nnn'nTGG -3 ! PflMI,AccB7I,Van91I >U
+;BauI 1 C'ACGA_G 4 ! BssSI,Bst2BI >F
+BbeI 5 G_GCGC'C -4 ! NarI,DinI,EgeI,EheI,KasI,Mly113I,SfoI >AK
+;Bbr7I 13 GAAGACnnnnnnn'nnnn_ 4 ! BbsI,BpiI,BpuAI,BstV2I >
+;BbrPI 3 CAC'GTG 0 ! PmaCI,AcvI,Eco72I,PmlI,PspCI >MO
+BbsI 8 GAAGACnn'nnnn_ 4 ! BpiI,BpuAI,BstV2I >N
+;BbuI 5 G_CATG'C -4 ! SphI,PaeI >R
+BbvI 13 GCAGCnnnnnnnn'nnnn_ 4 ! BseXI,BstV1I >N
+;BbvII 8 GAAGACnn'nnnn_ 4 ! BbsI,BpiI,BpuAI,BstV2I >
+;Bbv12I 5 G_wGCw'C -4 ! Alw21I,BsiHKAI >IV
+BbvCI 2 CC'TCA_GC 3 ! >N
+BccI 9 CCATCnnnn'n_ 1 ! >N
+;Bce83I 22 CTTGAGnnnnnnnnnnnnnn_nn' -2 ! BpuEI >
+BceAI 17 ACGGCnnnnnnnnnnnn'nn_ 2 ! >N
+;BcefI 17 ACGGCnnnnnnnnnnnn'n_ 1 ! BceAI >
+BcgI 24 CGAnnnnnnTGCnnnnnnnnnn_nn' -2 ! >N
+BcgI 24 GCAnnnnnnTCGnnnnnnnnnn_nn' -2 ! >N
+BciVI 12 GTATCCnnnnn_n' -1 ! BfuI >N
+BclI 1 T'GATC_A 4 ! FbaI,Ksp22I >FGJMNORSUWY
+;BcnI 2 CC's_GG 1 ! AsuC2I,BpuMI,NciI >FK
+;BcuI 1 A'CTAG_T 4 ! SpeI,AhlI >F
+BdaI 24 TGAnnnnnnTCAnnnnnnnnnn_nn' -2 ! >F
+;BetI 1 w'CCGG_w 4 ! BsaWI >
+BfaI 1 C'TA_G 2 ! MaeI,FspBI,XspI >N
+;BfiI 11 ACTGGGnnnn_n' -1 ! BmrI,BmuI >F
+;BfmI 1 C'TryA_G 4 ! BstSFI,SfcI >F
+;BfrI 1 C'TTAA_G 4 ! AflII,BspTI,Bst98I,MspCI,Vha464I >MO
+;BfuI 12 GTATCCnnnnn_n' -1 ! BciVI >F
+;BfuAI 10 ACCTGCnnnn'nnnn_ 4 ! BspMI,Acc36I,BveI >N
+;BfuCI 0 'GATC_ 4 ! MboI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >N
+BglI 7 GCCn_nnn'nGGC -3 ! >AFGHIJKMNOQRSUVWXY
+BglII 1 A'GATC_T 4 ! >ABFGHIJKMNOQRSUVWXY
+;BinI 9 GGATCnnnn'n_ 1 ! AclWI,AlwI,BspPI >
+BisI 2 GC'n_GC 1 ! BlsI,GluI >I
+;BlnI 1 C'CTAG_G 4 ! AvrII,AspA2I,XmaJI >AKMS
+BlpI 2 GC'TnA_GC 3 ! Bpu1102I,Bsp1720I,CelII >N
+BlsI 3 GC_n'GC -1 ! BisI,GluI >I
+;BmcAI 3 AGT'ACT 0 ! ScaI,AssI,ZrmI >V
+;Bme18I 1 G'GwC_C 3 ! AvaII,Eco47I,SinI,VpaK11BI >IV
+;Bme1390I 2 CC'n_GG 1 ! ScrFI,BmrFI,BssKI,BstSCI,MspR9I,StyD4I >F
+Bme1580I 5 G_kGCm'C -4 ! BseSI,BstSLI >N
+;BmeRI 6 GACnn_n'nnGTC -1 ! Eam1105I,AhdI,AspEI,DriI,EclHKI >V
+BmeT110I 2 Cy'CG_rG 2 ! AvaI,Ama87I,BsiHKCI,BsoBI,Eco88I >K
+;BmgI 3 GkGCCC 0 ? ! >
+BmgBI 3 CAC'GTC 0 ! BtrI,AjiI >N
+BmgT120I 2 GG'n_CC 1 ! AspS9I,Cfr13I,Sau96I >K
+;BmiI 3 GGn'nCC 0 ! NlaIV,BspLI,PspN4I >V
+BmrI 11 ACTGGGnnnn_n' -1 ! BfiI,BmuI >N
+;BmrFI 2 CC'n_GG 1 ! ScrFI,Bme1390I,BssKI,BstSCI,MspR9I,StyD4I >V
+BmtI 5 G_CTAG'C -4 ! NheI,AsuNHI,BspOI >INV
+;BmuI 11 ACTGGGnnnn_n' -1 ! BfiI,BmrI >I
+;BoxI 5 GACnn'nnGTC 0 ! PshAI,BstPAI >F
+;BpiI 8 GAAGACnn'nnnn_ 4 ! BbsI,BpuAI,BstV2I >F
+BplI 24 GAGnnnnnCTCnnnnnnnn_nnnnn' -5 ! >F
+BpmI 22 CTGGAGnnnnnnnnnnnnnn_nn' -2 ! GsuI >IN
+Bpu10I 2 CC'TnA_GC 3 ! >FINV
+;Bpu14I 2 TT'CG_AA 2 ! Bsp119I,BspT104I,BstBI,Csp45I,NspV,SfuI >IV
+;Bpu1102I 2 GC'TnA_GC 3 ! BlpI,Bsp1720I,CelII >AFK
+;BpuAI 8 GAAGACnn'nnnn_ 4 ! BbsI,BpiI,BstV2I >M
+BpuEI 22 CTTGAGnnnnnnnnnnnnnn_nn' -2 ! >N
+;BpuMI 2 CC's_GG 1 ! AsuC2I,BcnI,NciI >V
+;BpvUI 4 CG_AT'CG -2 ! PvuI,MvrI,Ple19I >V
+BsaI 7 GGTCTCn'nnnn_ 4 ! Eco31I,Bso31I,BspTNI >N
+;Bsa29I 2 AT'CG_AT 2 ! ClaI,BanIII,BseCI,BshVI,BspDI,BspXI,Bsu15I,BsuTUI >I
+BsaAI 3 yAC'GTr 0 ! BstBAI,Ppu21I >N
+BsaBI 5 GATnn'nnATC 0 ! Bse8I,BseJI,MamI >N
+BsaHI 2 Gr'CG_yC 2 ! AcyI,BssNI,BstACI,Hin1I,Hsp92I >N
+BsaJI 1 C'CnnG_G 4 ! BseDI,BssECI >N
+;BsaMI 7 GAATG_Cn' -2 ! BsmI,Mva1269I,PctI >GR
+BsaWI 1 w'CCGG_w 4 ! >N
+BsaXI 21 ACnnnnnCTCCnnnnnnn_nnn' -3 ! >N
+BsaXI 23 GGAGnnnnnGTnnnnnnnnn_nnn' -3 ! >N
+;BsbI 3 CAACAC 0 ? ! >
+;Bsc4I 7 CCnn_nnn'nnGG -3 ! BsiYI,AfiI,BseLI,BslI >I
+;BscAI 9 GCATCnnnn'nn_ 2 ! SfaNI,LweI >
+;BscGI 2 CCCGT 0 ? ! >
+;Bse1I 6 ACTG_Gn' -2 ! BsrI,BseNI,BsrSI >IV
+;Bse8I 5 GATnn'nnATC 0 ! BsaBI,BseJI,MamI >IV
+;Bse21I 2 CC'TnA_GG 3 ! AxyI,Bsu36I,Eco81I >IV
+;Bse118I 1 r'CCGG_y 4 ! Cfr10I,BsrFI,BssAI >IV
+;BseAI 1 T'CCGG_A 4 ! AccIII,Aor13HI,Bsp13I,BspEI,Kpn2I,MroI >CM
+;BseBI 2 CC'w_GG 1 ! EcoRII,AjnI,BstNI,BstOI,Bst2UI,MvaI,Psp6I,PspGI >C
+;BseCI 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BshVI,BspDI,BspXI,Bsu15I,BsuTUI >C
+;BseDI 1 C'CnnG_G 4 ! BsaJI,BssECI >F
+;Bse3DI 8 GCAATG_nn' -2 ! BsrDI,BseMI >IV
+;BseGI 7 GGATG_nn' -2 ! FokI,BstF5I,BtsCI >F
+;BseJI 5 GATnn'nnATC 0 ! BsaBI,Bse8I,MamI >F
+;BseLI 7 CCnn_nnn'nnGG -3 ! BsiYI,AfiI,Bsc4I,BslI >F
+;BseMI 8 GCAATG_nn' -2 ! BsrDI,Bse3DI >F
+BseMII 15 CTCAGnnnnnnnn_nn' -2 ! BspCNI >F
+;BseNI 6 ACTG_Gn' -2 ! BsrI,Bse1I,BsrSI >F
+;BsePI 1 G'CGCG_C 4 ! BssHII,PauI >IV
+BseRI 16 GAGGAGnnnnnnnn_nn' -2 ! >N
+;BseSI 5 G_kGCm'C -4 ! Bme1580I,BstSLI >F
+;BseXI 13 GCAGCnnnnnnnn'nnnn_ 4 ! BbvI,BstV1I >F
+;BseX3I 1 C'GGCC_G 4 ! BstZI,EagI,EclXI,Eco52I >IV
+BseYI 1 C'CCAG_C 4 ! >N
+BsgI 22 GTGCAGnnnnnnnnnnnnnn_nn' -2 ! >N
+;Bsh1236I 2 CG'CG 0 ! AccII,BspFNI,BstFNI,BstUI,MvnI >F
+;Bsh1285I 4 CG_ry'CG -2 ! BsiEI,BstMCI >F
+;BshFI 2 GG'CC 0 ! HaeIII,BsnI,BspANI,BsuRI,PhoI >C
+;BshNI 1 G'GyrC_C 4 ! AccB1I,BanI,BspT107I >F
+;BshTI 1 A'CCGG_T 4 ! AgeI,AsiGI,CspAI,PinAI >F
+;BshVI 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BseCI,BspDI,BspXI,Bsu15I,BsuTUI >V
+;BsiI 1 C'ACGA_G 4 ! BauI,BssSI,Bst2BI >
+BsiEI 4 CG_ry'CG -2 ! Bsh1285I,BstMCI >N
+BsiHKAI 5 G_wGCw'C -4 ! Alw21I,Bbv12I >N
+;BsiHKCI 1 C'yCGr_G 4 ! AvaI,Ama87I,BmeT110I,BsoBI,Eco88I >QX
+;BsiSI 1 C'CG_G 2 ! HpaII,HapII,MspI >C
+BsiWI 1 C'GTAC_G 4 ! Pfl23II,PspLI >MNO
+;BsiYI 7 CCnn_nnn'nnGG -3 ! AfiI,Bsc4I,BseLI,BslI >M
+BslI 7 CCnn_nnn'nnGG -3 ! BsiYI,AfiI,Bsc4I,BseLI >GNW
+;BslFI 15 GGGACnnnnnnnnnn'nnnn_ 4 ! BsmFI,FaqI >I
+BsmI 7 GAATG_Cn' -2 ! BsaMI,Mva1269I,PctI >JMNOSW
+BsmAI 6 GTCTCn'nnnn_ 4 ! Alw26I,BstMAI >N
+BsmBI 7 CGTCTCn'nnnn_ 4 ! Esp3I >N
+BsmFI 15 GGGACnnnnnnnnnn'nnnn_ 4 ! BslFI,FaqI >N
+;BsnI 2 GG'CC 0 ! HaeIII,BshFI,BspANI,BsuRI,PhoI >V
+;Bso31I 7 GGTCTCn'nnnn_ 4 ! Eco31I,BsaI,BspTNI >IV
+;BsoBI 1 C'yCGr_G 4 ! AvaI,Ama87I,BmeT110I,BsiHKCI,Eco88I >N
+;Bsp13I 1 T'CCGG_A 4 ! AccIII,Aor13HI,BseAI,BspEI,Kpn2I,MroI >IV
+;Bsp19I 1 C'CATG_G 4 ! NcoI >IV
+;Bsp24I 24 GACnnnnnnTGGnnnnnnn_nnnnn' -5 ! >
+;Bsp24I 25 CCAnnnnnnGTCnnnnnnnn_nnnnn' -5 ! >
+;Bsp68I 3 TCG'CGA 0 ! NruI,BtuMI >F
+;Bsp119I 2 TT'CG_AA 2 ! Bpu14I,BspT104I,BstBI,Csp45I,NspV,SfuI >F
+;Bsp120I 1 G'GGCC_C 4 ! ApaI,PspOMI >F
+;Bsp143I 0 'GATC_ 4 ! MboI,BfuCI,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >F
+Bsp1286I 5 G_dGCh'C -4 ! SduI,MhlI >JKNR
+;Bsp1407I 1 T'GTAC_A 4 ! BsrGI,BstAUI >FK
+;Bsp1720I 2 GC'TnA_GC 3 ! BlpI,Bpu1102I,CelII >IV
+;BspACI 1 C'CG_C 2 ! AciI,SsiI >I
+;BspANI 2 GG'CC 0 ! HaeIII,BshFI,BsnI,BsuRI,PhoI >X
+BspCNI 14 CTCAGnnnnnnn_nn' -2 ! BseMII >N
+;BspDI 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BseCI,BshVI,BspXI,Bsu15I,BsuTUI >N
+BspEI 1 T'CCGG_A 4 ! AccIII,Aor13HI,BseAI,Bsp13I,Kpn2I,MroI >N
+;BspFNI 2 CG'CG 0 ! AccII,Bsh1236I,BstFNI,BstUI,MvnI >I
+;BspGI 3 CTGGAC 0 ? ! >
+BspHI 1 T'CATG_A 4 ! PagI,RcaI >N
+;BspLI 3 GGn'nCC 0 ! NlaIV,BmiI,PspN4I >F
+;BspLU11I 1 A'CATG_T 4 ! PciI,PscI >M
+BspMI 10 ACCTGCnnnn'nnnn_ 4 ! Acc36I,BfuAI,BveI >N
+;BspMII 1 T'CCGG_A 4 ! AccIII,Aor13HI,BseAI,Bsp13I,BspEI,Kpn2I,MroI >
+;BspMAI 5 C_TGCA'G -4 ! PstI >X
+;BspNCI 2 CCAGA 0 ? ! >
+;BspOI 5 G_CTAG'C -4 ! NheI,AsuNHI,BmtI >F
+;BspPI 9 GGATCnnnn'n_ 1 ! AclWI,AlwI >F
+;BspQI 8 GCTCTTCn'nnn_ 3 ! SapI,LguI,PciSI >N
+;BspTI 1 C'TTAA_G 4 ! AflII,BfrI,Bst98I,MspCI,Vha464I >F
+;BspT104I 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BstBI,Csp45I,NspV,SfuI >K
+;BspT107I 1 G'GyrC_C 4 ! AccB1I,BanI,BshNI >K
+;BspTNI 7 GGTCTCn'nnnn_ 4 ! Eco31I,BsaI,Bso31I >QX
+;BspXI 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BseCI,BshVI,BspDI,Bsu15I,BsuTUI >GW
+BsrI 6 ACTG_Gn' -2 ! Bse1I,BseNI,BsrSI >N
+BsrBI 3 CCG'CTC 0 ! AccBSI,MbiI >N
+BsrDI 8 GCAATG_nn' -2 ! Bse3DI,BseMI >N
+BsrFI 1 r'CCGG_y 4 ! Cfr10I,Bse118I,BssAI >N
+BsrGI 1 T'GTAC_A 4 ! Bsp1407I,BstAUI >N
+;BsrSI 6 ACTG_Gn' -2 ! BsrI,Bse1I,BseNI >R
+;BssAI 1 r'CCGG_y 4 ! Cfr10I,Bse118I,BsrFI >C
+;BssECI 1 C'CnnG_G 4 ! BsaJI,BseDI >I
+BssHII 1 G'CGCG_C 4 ! BsePI,PauI >AJKMNOQRSX
+;BssKI 0 'CCnGG_ 5 ! ScrFI,Bme1390I,BmrFI,BstSCI,MspR9I,StyD4I >N
+;BssMI 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BstKTI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >V
+;BssNI 2 Gr'CG_yC 2 ! AcyI,BsaHI,BstACI,Hin1I,Hsp92I >V
+;BssNAI 3 GTA'TAC 0 ! Bst1107I,BstZ17I >IV
+BssSI 1 C'ACGA_G 4 ! BauI,Bst2BI >N
+;BssT1I 1 C'CwwG_G 4 ! StyI,Eco130I,EcoT14I,ErhI >IV
+;Bst6I 7 CTCTTCn'nnn_ 3 ! Ksp632I,Eam1104I,EarI >IV
+;Bst98I 1 C'TTAA_G 4 ! AflII,BfrI,BspTI,MspCI,Vha464I >R
+;Bst1107I 3 GTA'TAC 0 ! BssNAI,BstZ17I >FKM
+;BstACI 2 Gr'CG_yC 2 ! AcyI,BsaHI,BssNI,Hin1I,Hsp92I >I
+BstAPI 7 GCAn_nnn'nTGC -3 ! >IN
+;BstAUI 1 T'GTAC_A 4 ! Bsp1407I,BsrGI >IV
+BstBI 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BspT104I,Csp45I,NspV,SfuI >N
+;Bst2BI 1 C'ACGA_G 4 ! BauI,BssSI >IV
+;BstBAI 3 yAC'GTr 0 ! BsaAI,Ppu21I >IV
+;Bst4CI 3 AC_n'GT -1 ! HpyCH4III,TaaI >IV
+;BstC8I 3 GCn'nGC 0 ! Cac8I >I
+;BstDEI 1 C'TnA_G 3 ! DdeI,HpyF3I >IV
+;BstDSI 1 C'CryG_G 4 ! BtgI >IV
+BstEII 1 G'GTnAC_C 5 ! BstPI,Eco91I,EcoO65I,PspEI >GHJMNORSUW
+;BstENI 5 CCTnn'n_nnAGG 1 ! EcoNI,XagI >IV
+;BstF5I 7 GGATG_nn' -2 ! FokI,BseGI,BtsCI >IV
+;BstFNI 2 CG'CG 0 ! AccII,Bsh1236I,BspFNI,BstUI,MvnI >IV
+;BstH2I 5 r_GCGC'y -4 ! HaeII >IV
+;BstHHI 3 G_CG'C -2 ! HhaI,AspLEI,CfoI,Hin6I,HinP1I,HspAI >IV
+BstKTI 3 G_AT'C -2 ! MboI,BfuCI,Bsp143I,BssMI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >I
+;BstMAI 6 GTCTCn'nnnn_ 4 ! BsmAI,Alw26I >IV
+;BstMBI 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,DpnII,Kzo9I,NdeII,Sau3AI >IV
+;BstMCI 4 CG_ry'CG -2 ! Bsh1285I,BsiEI >IV
+;BstMWI 7 GCnn_nnn'nnGC -3 ! MwoI,HpyF10VI >I
+BstNI 2 CC'w_GG 1 ! EcoRII,AjnI,BseBI,BstOI,Bst2UI,MvaI,Psp6I,PspGI >N
+;BstNSI 5 r_CATG'y -4 ! NspI,XceI >IV
+;BstOI 2 CC'w_GG 1 ! EcoRII,AjnI,BseBI,BstNI,Bst2UI,MvaI,Psp6I,PspGI >R
+;BstPI 1 G'GTnAC_C 5 ! BstEII,Eco91I,EcoO65I,PspEI >K
+;BstPAI 5 GACnn'nnGTC 0 ! PshAI,BoxI >IV
+;BstSCI 0 'CCnGG_ 5 ! ScrFI,Bme1390I,BmrFI,BssKI,MspR9I,StyD4I >I
+;BstSFI 1 C'TryA_G 4 ! BfmI,SfcI >I
+;BstSLI 5 G_kGCm'C -4 ! BseSI,Bme1580I >I
+;BstSNI 3 TAC'GTA 0 ! SnaBI,Eco105I >IV
+BstUI 2 CG'CG 0 ! AccII,Bsh1236I,BspFNI,BstFNI,MvnI >N
+;Bst2UI 2 CC'w_GG 1 ! EcoRII,AjnI,BseBI,BstNI,BstOI,MvaI,Psp6I,PspGI >IV
+;BstV1I 13 GCAGCnnnnnnnn'nnnn_ 4 ! BbvI,BseXI >I
+;BstV2I 8 GAAGACnn'nnnn_ 4 ! BbsI,BpiI,BpuAI >IV
+BstXI 8 CCAn_nnnn'nTGG -4 ! >AFGHIJKMNOQRVWX
+;BstX2I 1 r'GATC_y 4 ! XhoII,BstYI,MflI,PsuI >IV
+BstYI 1 r'GATC_y 4 ! XhoII,BstX2I,MflI,PsuI >N
+;BstZI 1 C'GGCC_G 4 ! BseX3I,EagI,EclXI,Eco52I >R
+BstZ17I 3 GTA'TAC 0 ! BssNAI,Bst1107I >N
+;Bsu15I 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BseCI,BshVI,BspDI,BspXI,BsuTUI >F
+Bsu36I 2 CC'TnA_GG 3 ! AxyI,Bse21I,Eco81I >NR
+;BsuRI 2 GG'CC 0 ! HaeIII,BshFI,BsnI,BspANI,PhoI >FI
+;BsuTUI 2 AT'CG_AT 2 ! ClaI,BanIII,Bsa29I,BseCI,BshVI,BspDI,BspXI,Bsu15I >X
+BtgI 1 C'CryG_G 4 ! BstDSI >N
+BtgZI 16 GCGATGnnnnnnnnnn'nnnn_ 4 ! >N
+;BthCI 4 G_CnG'C -3 ! Fnu4HI,Fsp4HI,ItaI,SatI >
+;BtrI 3 CAC'GTC 0 ! AjiI,BmgBI >IV
+BtsI 8 GCAGTG_nn' -2 ! >N
+BtsCI 7 GGATG_nn' -2 ! FokI,BseGI,BstF5I >N
+;BtuMI 3 TCG'CGA 0 ! NruI,Bsp68I >V
+;BveI 10 ACCTGCnnnn'nnnn_ 4 ! BspMI,Acc36I,BfuAI >F
+Cac8I 3 GCn'nGC 0 ! BstC8I >N
+;CaiI 6 CAG_nnn'CTG -3 ! AlwNI >F
+;CauII 2 CC's_GG 1 ! AsuC2I,BcnI,BpuMI,NciI >
+;CciNI 2 GC'GGCC_GC 4 ! NotI >IV
+;CdiI 4 CATC'G 0 ! >
+;CelII 2 GC'TnA_GC 3 ! BlpI,Bpu1102I,Bsp1720I >M
+;CfoI 3 G_CG'C -2 ! HhaI,AspLEI,BstHHI,Hin6I,HinP1I,HspAI >MRS
+;CfrI 1 y'GGCC_r 4 ! AcoI,EaeI >F
+;Cfr9I 1 C'CCGG_G 4 ! SmaI,TspMI,XmaI,XmaCI >FO
+;Cfr10I 1 r'CCGG_y 4 ! Bse118I,BsrFI,BssAI >FGKO
+;Cfr13I 1 G'GnC_C 3 ! AspS9I,BmgT120I,Sau96I >AFO
+;Cfr42I 4 CC_GC'GG -2 ! SacII,KspI,Sfr303I,SgrBI,SstII >F
+;ChaI 4 _GATC' -4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >
+;CjeI 26 CCAnnnnnnGTnnnnnnnnn_nnnnnn' -6 ! >
+;CjeI 25 ACnnnnnnTGGnnnnnnnn_nnnnnn' -6 ! >
+;CjeNII 5 GAGnnnnnGT 0 ? ! >
+;CjePI 26 CCAnnnnnnnTCnnnnnnnn_nnnnnn' -6 ! >
+;CjePI 25 GAnnnnnnnTGGnnnnnnn_nnnnnn' -6 ! >
+;CjuI 5 CAynnnnnrTG 0 ? ! >
+;CjuII 5 CAynnnnnCTC 0 ? ! >
+ClaI 2 AT'CG_AT 2 ! BanIII,Bsa29I,BseCI,BshVI,BspDI,BspXI,Bsu15I,BsuTUI >ABHKMNRSU
+;CpoI 2 CG'GwC_CG 3 ! RsrII,CspI,Rsr2I >AFK
+;CseI 10 GACGCnnnnn'nnnnn_ 5 ! HgaI >F
+;CspI 2 CG'GwC_CG 3 ! RsrII,CpoI,Rsr2I >OR
+;Csp6I 1 G'TA_C 2 ! RsaI,AfaI,CviQI,RsaNI >F
+;Csp45I 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BspT104I,BstBI,NspV,SfuI >OR
+;CspAI 1 A'CCGG_T 4 ! AgeI,AsiGI,BshTI,PinAI >C
+CspCI 24 CAAnnnnnGTGGnnnnnnnnnn_nn' -2 ! >N
+CspCI 25 CCACnnnnnTTGnnnnnnnnnnn_nn' -2 ! >N
+;CstMI 26 AAGGAGnnnnnnnnnnnnnnnnnn_nn' -2 ! >
+CviAII 1 C'AT_G 2 ! NlaIII,FaeI,FatI,Hin1II,Hsp92II >N
+;CviJI 2 rG'Cy 0 ! CviKI-1 >QX
+CviKI-1 2 rG'Cy 0 ! CviJI >N
+CviQI 1 G'TA_C 2 ! RsaI,AfaI,Csp6I,RsaNI >N
+;CviRI 2 TG'CA 0 ! HpyCH4V >
+DdeI 1 C'TnA_G 3 ! BstDEI,HpyF3I >BGMNORSW
+;DinI 3 GGC'GCC 0 ! NarI,BbeI,EgeI,EheI,KasI,Mly113I,SfoI >V
+DpnI 2 GA'TC 0 ! MalI >BEFGMNRSW
+;DpnII 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,Kzo9I,NdeII,Sau3AI >N
+DraI 3 TTT'AAA 0 ! >ABFGIJKMNOQRSUVWXY
+;DraII 2 rG'GnC_Cy 3 ! EcoO109I >GMW
+DraIII 6 CAC_nnn'GTG -3 ! AdeI >GIMNVW
+DrdI 7 GACnn_nn'nnGTC -2 ! AasI,DseDI >N
+;DrdII 3 GAACCA 0 ? ! >
+;DriI 6 GACnn_n'nnGTC -1 ! Eam1105I,AhdI,AspEI,BmeRI,EclHKI >I
+;DsaI 1 C'CryG_G 4 ! BstDSI,BtgI >
+;DseDI 7 GACnn_nn'nnGTC -2 ! DrdI,AasI >IV
+EaeI 1 y'GGCC_r 4 ! CfrI,AcoI >AKMN
+EagI 1 C'GGCC_G 4 ! BseX3I,BstZI,EclXI,Eco52I >GNW
+;Eam1104I 7 CTCTTCn'nnn_ 3 ! Ksp632I,Bst6I,EarI >F
+;Eam1105I 6 GACnn_n'nnGTC -1 ! AhdI,AspEI,BmeRI,DriI,EclHKI >FK
+EarI 7 CTCTTCn'nnn_ 3 ! Ksp632I,Bst6I,Eam1104I >N
+EciI 17 GGCGGAnnnnnnnnn_nn' -2 ! >N
+;Ecl136II 3 GAG'CTC 0 ! SacI,EcoICRI,Psp124BI,SstI >F
+;EclHKI 6 GACnn_n'nnGTC -1 ! Eam1105I,AhdI,AspEI,BmeRI,DriI >R
+;EclXI 1 C'GGCC_G 4 ! BseX3I,BstZI,EagI,Eco52I >MS
+;Eco24I 5 G_rGCy'C -4 ! BanII,EcoT38I,FriOI >F
+;Eco31I 7 GGTCTCn'nnnn_ 4 ! BsaI,Bso31I,BspTNI >F
+;Eco32I 3 GAT'ATC 0 ! EcoRV >F
+;Eco47I 1 G'GwC_C 3 ! AvaII,Bme18I,SinI,VpaK11BI >FO
+;Eco47III 3 AGC'GCT 0 ! AfeI,Aor51HI >FGMORW
+;Eco52I 1 C'GGCC_G 4 ! BseX3I,BstZI,EagI,EclXI >FKO
+;Eco57I 22 CTGAAGnnnnnnnnnnnnnn_nn' -2 ! AcuI >F
+;Eco72I 3 CAC'GTG 0 ! PmaCI,AcvI,BbrPI,PmlI,PspCI >F
+;Eco81I 2 CC'TnA_GG 3 ! AxyI,Bse21I,Bsu36I >AFKO
+;Eco88I 1 C'yCGr_G 4 ! AvaI,Ama87I,BmeT110I,BsiHKCI,BsoBI >F
+;Eco91I 1 G'GTnAC_C 5 ! BstEII,BstPI,EcoO65I,PspEI >F
+;Eco105I 3 TAC'GTA 0 ! SnaBI,BstSNI >FO
+;Eco130I 1 C'CwwG_G 4 ! StyI,BssT1I,EcoT14I,ErhI >F
+;Eco147I 3 AGG'CCT 0 ! StuI,AatI,PceI,SseBI >F
+;EcoHI 0 'CCsGG_ 5 ! AsuC2I,BcnI,BpuMI,NciI >
+EcoICRI 3 GAG'CTC 0 ! SacI,Ecl136II,Psp124BI,SstI >IRV
+Eco57MI 22 CTGrAGnnnnnnnnnnnnnn_nn' -2 ! >F
+EcoNI 5 CCTnn'n_nnAGG 1 ! BstENI,XagI >N
+;EcoO65I 1 G'GTnAC_C 5 ! BstEII,BstPI,Eco91I,PspEI >K
+EcoO109I 2 rG'GnC_Cy 3 ! DraII >AFJKN
+EcoRI 1 G'AATT_C 4 ! >ABCFGHIJKMNOQRSUVWXY
+;EcoRII 0 'CCwGG_ 5 ! AjnI,BseBI,BstNI,BstOI,Bst2UI,MvaI,Psp6I,PspGI >FJMOS
+EcoRV 3 GAT'ATC 0 ! Eco32I >ABCGHIJKMNOQRSUVWXY
+;EcoT14I 1 C'CwwG_G 4 ! StyI,BssT1I,Eco130I,ErhI >K
+;EcoT22I 5 A_TGCA'T -4 ! Mph1103I,NsiI,Zsp2I >AKO
+;EcoT38I 5 G_rGCy'C -4 ! BanII,Eco24I,FriOI >J
+;EgeI 3 GGC'GCC 0 ! NarI,BbeI,DinI,EheI,KasI,Mly113I,SfoI >I
+;EheI 3 GGC'GCC 0 ! NarI,BbeI,DinI,EgeI,KasI,Mly113I,SfoI >FO
+;ErhI 1 C'CwwG_G 4 ! StyI,BssT1I,Eco130I,EcoT14I >IV
+;EsaBC3I 2 TC'GA 0 ! TaqI >
+;EspI 2 GC'TnA_GC 3 ! BlpI,Bpu1102I,Bsp1720I,CelII >
+;Esp3I 7 CGTCTCn'nnnn_ 4 ! BsmBI >F
+;FaeI 4 _CATG' -4 ! NlaIII,CviAII,FatI,Hin1II,Hsp92II >I
+FalI 24 AAGnnnnnCTTnnnnnnnn_nnnnn' -5 ! >I
+;FaqI 15 GGGACnnnnnnnnnn'nnnn_ 4 ! BslFI,BsmFI >F
+FatI 0 'CATG_ 4 ! NlaIII,CviAII,FaeI,Hin1II,Hsp92II >IN
+FauI 9 CCCGCnnnn'nn_ 2 ! SmuI >IN
+;FauNDI 2 CA'TA_TG 2 ! NdeI >IV
+;FbaI 1 T'GATC_A 4 ! BclI,Ksp22I >AK
+;FblI 2 GT'mk_AC 2 ! AccI,XmiI >IV
+;FinI 2 GGGAC 0 ? ! BslFI,BsmFI,FaqI >
+;FmuI 4 G_GnC'C -3 ! AspS9I,BmgT120I,Cfr13I,Sau96I >
+;FnuDII 2 CG'CG 0 ! AccII,Bsh1236I,BspFNI,BstFNI,BstUI,MvnI >
+Fnu4HI 2 GC'n_GC 1 ! Fsp4HI,ItaI,SatI >N
+FokI 14 GGATGnnnnnnnnn'nnnn_ 4 ! BseGI,BstF5I,BtsCI >AGIJKMNQRVWX
+;FriOI 5 G_rGCy'C -4 ! BanII,Eco24I,EcoT38I >IV
+FseI 6 GG_CCGG'CC -4 ! RigI >AN
+FspI 3 TGC'GCA 0 ! Acc16I,AviII,NsbI >JNO
+FspAI 4 rTGC'GCAy 0 ! >F
+;FspBI 1 C'TA_G 2 ! MaeI,BfaI,XspI >F
+;Fsp4HI 2 GC'n_GC 1 ! Fnu4HI,ItaI,SatI >I
+;GdiII 1 C'GGCC_r 4 ! >
+GlaI 2 GC'GC 0 ! >I
+GluI 2 GC'nG_C 2 ! BisI,BlsI >I
+;GsuI 22 CTGGAGnnnnnnnnnnnnnn_nn' -2 ! BpmI >F
+;HaeI 3 wGG'CCw 0 ! >
+HaeII 5 r_GCGC'y -4 ! BstH2I >GJKMNORSW
+HaeIII 2 GG'CC 0 ! BshFI,BsnI,BspANI,BsuRI,PhoI >ABGHIJKMNOQRSUWXY
+;HaeIV 25 GAynnnnnrTCnnnnnnnnn_nnnnn' -5 ! >
+;HaeIV 24 GAynnnnnrTCnnnnnnn_nnnnnn' -6 ! >
+;HapII 1 C'CG_G 2 ! HpaII,BsiSI,MspI >AK
+HgaI 10 GACGCnnnnn'nnnnn_ 5 ! CseI >IN
+;HgiAI 5 G_wGCw'C -4 ! Alw21I,Bbv12I,BsiHKAI >
+;HgiCI 1 G'GyrC_C 4 ! AccB1I,BanI,BshNI,BspT107I >
+;HgiEII 6 ACCnnnnnnGGT 0 ? ! >
+;HgiJII 5 G_rGCy'C -4 ! BanII,Eco24I,EcoT38I,FriOI >
+HhaI 3 G_CG'C -2 ! AspLEI,BstHHI,CfoI,Hin6I,HinP1I,HspAI >ABFGJKNORUWY
+;Hin1I 2 Gr'CG_yC 2 ! AcyI,BsaHI,BssNI,BstACI,Hsp92I >FKO
+;Hin1II 4 _CATG' -4 ! NlaIII,CviAII,FaeI,FatI,Hsp92II >F
+Hin4I 24 GAynnnnnvTCnnnnnnnn_nnnnn' -5 ! >F
+Hin4I 24 GAbnnnnnrTCnnnnnnnn_nnnnn' -5 ! >F
+;Hin4II 11 CCTTCnnnnn_n' -1 ! HpyAV >
+;Hin6I 1 G'CG_C 2 ! HhaI,AspLEI,BstHHI,CfoI,HinP1I,HspAI >F
+HinP1I 1 G'CG_C 2 ! HhaI,AspLEI,BstHHI,CfoI,Hin6I,HspAI >N
+HincII 3 GTy'rAC 0 ! HindII >ABFGHJKNOQRUWXY
+;HindII 3 GTy'rAC 0 ! HincII >IMSV
+HindIII 1 A'AGCT_T 4 ! >ABCFGHIJKMNOQRSUVWXY
+HinfI 1 G'AnT_C 3 ! >ABCFGHIJKMNOQRUVWXY
+HpaI 3 GTT'AAC 0 ! KspAI >ABCGHIJKMNOQRSUVWX
+HpaII 1 C'CG_G 2 ! BsiSI,HapII,MspI >BFGIMNOQRSUVWX
+HphI 13 GGTGAnnnnnnn_n' -1 ! AsuHPI >FN
+Hpy8I 3 GTn'nAC 0 ! >F
+Hpy99I 5 _CGwCG' -5 ! >N
+;Hpy178III 2 TC'nn_GA 2 ! Hpy188III >
+Hpy188I 3 TC_n'GA -1 ! >N
+Hpy188III 2 TC'nn_GA 2 ! >N
+HpyAV 11 CCTTCnnnnn_n' -1 ! >N
+HpyCH4III 3 AC_n'GT -1 ! Bst4CI,TaaI >N
+HpyCH4IV 1 A'CG_T 2 ! MaeII,TaiI >N
+HpyCH4V 2 TG'CA 0 ! >N
+;HpyF3I 1 C'TnA_G 3 ! DdeI,BstDEI >F
+;HpyF10VI 7 GCnn_nnn'nnGC -3 ! MwoI,BstMWI >F
+;Hsp92I 2 Gr'CG_yC 2 ! AcyI,BsaHI,BssNI,BstACI,Hin1I >R
+;Hsp92II 4 _CATG' -4 ! NlaIII,CviAII,FaeI,FatI,Hin1II >R
+;HspAI 1 G'CG_C 2 ! HhaI,AspLEI,BstHHI,CfoI,Hin6I,HinP1I >IV
+;ItaI 2 GC'n_GC 1 ! Fnu4HI,Fsp4HI,SatI >M
+KasI 1 G'GCGC_C 4 ! NarI,BbeI,DinI,EgeI,EheI,Mly113I,SfoI >N
+KpnI 5 G_GTAC'C -4 ! Acc65I,Asp718I >ABCFGHIJKMNOQRSUVWXY
+;Kpn2I 1 T'CCGG_A 4 ! AccIII,Aor13HI,BseAI,Bsp13I,BspEI,MroI >F
+;KspI 4 CC_GC'GG -2 ! SacII,Cfr42I,Sfr303I,SgrBI,SstII >MS
+;Ksp22I 1 T'GATC_A 4 ! BclI,FbaI >IV
+;Ksp632I 7 CTCTTCn'nnn_ 3 ! Bst6I,Eam1104I,EarI >M
+;KspAI 3 GTT'AAC 0 ! HpaI >F
+;Kzo9I 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,NdeII,Sau3AI >I
+;LguI 8 GCTCTTCn'nnn_ 3 ! SapI,BspQI,PciSI >F
+;LpnI 3 rGC'GCy 0 ! HaeII,BstH2I >
+;LweI 10 GCATCnnnnn'nnnn_ 4 ! SfaNI >F
+;MabI 1 A'CCwGG_T 5 ! SexAI >I
+;MaeI 1 C'TA_G 2 ! BfaI,FspBI,XspI >M
+;MaeII 1 A'CG_T 2 ! HpyCH4IV,TaiI >M
+MaeIII 0 'GTnAC_ 5 ! >M
+;MalI 2 GA'TC 0 ! DpnI >I
+;MamI 5 GATnn'nnATC 0 ! BsaBI,Bse8I,BseJI >M
+;MauBI 4 CGCGCGCG 0 ? ! >
+;MbiI 3 CCG'CTC 0 ! BsrBI,AccBSI >F
+MboI 0 'GATC_ 4 ! BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,NdeII,Sau3AI >ABCFGKNQRUWXY
+MboII 13 GAAGAnnnnnnn_n' -1 ! >AFGIJKNOQRVWX
+;McaTI 4 GC_GC'GC -2 ! BsePI,BssHII,PauI >
+;McrI 4 CG_ry'CG -2 ! Bsh1285I,BsiEI,BstMCI >
+MfeI 1 C'AATT_G 4 ! MunI >N
+;MflI 1 r'GATC_y 4 ! XhoII,BstX2I,BstYI,PsuI >K
+;MhlI 5 G_dGCh'C -4 ! SduI,Bsp1286I >IV
+;MjaIV 3 GTnnAC 0 ? ! Hpy8I >
+;MlsI 3 TGG'CCA 0 ! BalI,MluNI,MscI,Msp20I >F
+MluI 1 A'CGCG_T 4 ! >ABFGHIJKMNOQRSUVWX
+;MluNI 3 TGG'CCA 0 ! BalI,MlsI,MscI,Msp20I >MS
+MlyI 10 GAGTCnnnnn' 0 ! PleI,PpsI,SchI >N
+;Mly113I 2 GG'CG_CC 2 ! NarI,BbeI,DinI,EgeI,EheI,KasI,SfoI >I
+MmeI 26 TCCrACnnnnnnnnnnnnnnnnnn_nn' -2 ! >NX
+MnlI 11 CCTCnnnnnn_n' -1 ! >FGINQVWX
+;Mph1103I 5 A_TGCA'T -4 ! EcoT22I,NsiI,Zsp2I >F
+MreI 2 CG'CCGG_CG 4 ! >F
+;MroI 1 T'CCGG_A 4 ! AccIII,Aor13HI,BseAI,Bsp13I,BspEI,Kpn2I >MO
+;MroNI 1 G'CCGG_C 4 ! NaeI,NgoMIV,PdiI >IV
+;MroXI 5 GAAnn'nnTTC 0 ! XmnI,Asp700I,PdmI >IV
+MscI 3 TGG'CCA 0 ! BalI,MlsI,MluNI,Msp20I >BNO
+MseI 1 T'TA_A 2 ! Tru1I,Tru9I >BN
+MslI 5 CAynn'nnrTG 0 ! RseI,SmiMI >N
+;MspI 1 C'CG_G 2 ! HpaII,BsiSI,HapII >AFGHIJKMNOQRSUVWXY
+;Msp20I 3 TGG'CCA 0 ! BalI,MlsI,MluNI,MscI >IV
+MspA1I 3 CmG'CkG 0 ! >INRV
+;MspCI 1 C'TTAA_G 4 ! AflII,BfrI,BspTI,Bst98I,Vha464I >C
+;MspR9I 2 CC'n_GG 1 ! ScrFI,Bme1390I,BmrFI,BssKI,BstSCI,StyD4I >I
+;MssI 4 GTTT'AAAC 0 ! PmeI >F
+;MstI 3 TGC'GCA 0 ! Acc16I,AviII,FspI,NsbI >
+;MunI 1 C'AATT_G 4 ! MfeI >FKM
+;MvaI 2 CC'w_GG 1 ! EcoRII,AjnI,BseBI,BstNI,BstOI,Bst2UI,Psp6I,PspGI >AFGKMOSW
+;Mva1269I 7 GAATG_Cn' -2 ! BsmI,BsaMI,PctI >F
+;MvnI 2 CG'CG 0 ! AccII,Bsh1236I,BspFNI,BstFNI,BstUI >M
+;MvrI 4 CG_AT'CG -2 ! PvuI,BpvUI,Ple19I >U
+MwoI 7 GCnn_nnn'nnGC -3 ! BstMWI,HpyF10VI >N
+NaeI 3 GCC'GGC 0 ! MroNI,NgoMIV,PdiI >ACKMNORU
+NarI 2 GG'CG_CC 2 ! BbeI,DinI,EgeI,EheI,KasI,Mly113I,SfoI >GJMNOQRUWX
+NciI 2 CC's_GG 1 ! AsuC2I,BcnI,BpuMI >GJNORSW
+NcoI 1 C'CATG_G 4 ! Bsp19I >ABCFGHJKMNOQRSUWXY
+NdeI 2 CA'TA_TG 2 ! FauNDI >ABFGJKMNQRSWXY
+;NdeII 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,Sau3AI >GJMRSW
+NgoMIV 1 G'CCGG_C 4 ! NaeI,MroNI,PdiI >NR
+NheI 1 G'CTAG_C 4 ! AsuNHI,BmtI,BspOI >ABFGJKMNORSUW
+NlaIII 4 _CATG' -4 ! CviAII,FaeI,FatI,Hin1II,Hsp92II >GNW
+NlaIV 3 GGn'nCC 0 ! BmiI,BspLI,PspN4I >GNW
+;Nli3877I 5 C_yCGr'G -4 ! AvaI,Ama87I,BmeT110I,BsiHKCI,BsoBI,Eco88I >
+NmeAIII 27 GCCGAGnnnnnnnnnnnnnnnnnnn_nn' -2 ! >N
+;NmeDI 13 rCCGGynnnnnnn'nnnnn_ 5 ! Cfr10I,Bse118I,BsrFI,BssAI >
+;NmuCI 0 'GTsAC_ 5 ! Tsp45I >F
+NotI 2 GC'GGCC_GC 4 ! CciNI >ABCFGHJKMNOQRSUWXY
+NruI 3 TCG'CGA 0 ! Bsp68I,BtuMI >ABCGIJKMNOQRSUWX
+;NsbI 3 TGC'GCA 0 ! Acc16I,AviII,FspI >FK
+NsiI 5 A_TGCA'T -4 ! EcoT22I,Mph1103I,Zsp2I >BGHJMNRSUW
+NspI 5 r_CATG'y -4 ! BstNSI,XceI >MN
+;NspV 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BspT104I,BstBI,Csp45I,SfuI >JO
+;NspBII 3 CmG'CkG 0 ! MspA1I >
+;OliI 5 CACnn'nnGTG 0 ! AleI >F
+;PabI 3 G_TA'C -2 ! RsaI,AfaI,Csp6I,CviQI,RsaNI >
+PacI 5 TTA_AT'TAA -2 ! >GNOW
+;PaeI 5 G_CATG'C -4 ! SphI,BbuI >F
+;PaeR7I 1 C'TCGA_G 4 ! XhoI,Sfr274I,SlaI,StrI,TliI >N
+;PagI 1 T'CATG_A 4 ! BspHI,RcaI >F
+;PalAI 2 GG'CGCG_CC 4 ! AscI,SgsI >I
+PasI 2 CC'CwG_GG 3 ! >F
+;PauI 1 G'CGCG_C 4 ! BsePI,BssHII >F
+;PceI 3 AGG'CCT 0 ! StuI,AatI,Eco147I,SseBI >IV
+PciI 1 A'CATG_T 4 ! BspLU11I,PscI >IN
+;PciSI 8 GCTCTTCn'nnn_ 3 ! SapI,BspQI,LguI >I
+;PctI 7 GAATG_Cn' -2 ! BsmI,BsaMI,Mva1269I >IV
+;PdiI 3 GCC'GGC 0 ! NaeI,MroNI,NgoMIV >F
+;PdmI 5 GAAnn'nnTTC 0 ! XmnI,Asp700I,MroXI >F
+;PfeI 1 G'AwT_C 3 ! TfiI >F
+;Pfl23II 1 C'GTAC_G 4 ! BsiWI,PspLI >F
+;Pfl1108I 3 TCGTAG 0 ? ! >
+;PflFI 4 GACn'n_nGTC 1 ! Tth111I,AspI,PsyI >N
+PflMI 7 CCAn_nnn'nTGG -3 ! AccB7I,BasI,Van91I >N
+PfoI 1 T'CCnGG_A 5 ! >F
+;PhoI 2 GG'CC 0 ! HaeIII,BshFI,BsnI,BspANI,BsuRI >N
+;PinAI 1 A'CCGG_T 4 ! AgeI,AsiGI,BshTI,CspAI >BM
+PleI 9 GAGTCnnnn'n_ 1 ! MlyI,PpsI,SchI >N
+;Ple19I 4 CG_AT'CG -2 ! PvuI,BpvUI,MvrI >I
+;PmaCI 3 CAC'GTG 0 ! AcvI,BbrPI,Eco72I,PmlI,PspCI >AK
+PmeI 4 GTTT'AAAC 0 ! MssI >GNW
+PmlI 3 CAC'GTG 0 ! PmaCI,AcvI,BbrPI,Eco72I,PspCI >N
+PpiI 25 GAACnnnnnCTCnnnnnnnn_nnnnn' -5 ! >F
+PpiI 24 GAGnnnnnGTTCnnnnnnn_nnnnn' -5 ! >F
+;PpsI 9 GAGTCnnnn'n_ 1 ! PleI,MlyI,SchI >I
+;Ppu10I 1 A'TGCA_T 4 ! EcoT22I,Mph1103I,NsiI,Zsp2I >
+;Ppu21I 3 yAC'GTr 0 ! BsaAI,BstBAI >F
+PpuMI 2 rG'GwC_Cy 3 ! Psp5II,PspPPI >NO
+;PscI 1 A'CATG_T 4 ! BspLU11I,PciI >F
+PshAI 5 GACnn'nnGTC 0 ! BoxI,BstPAI >AKN
+;PshBI 2 AT'TA_AT 2 ! VspI,AseI >K
+PsiI 3 TTA'TAA 0 ! >IN
+;Psp03I 4 G_GwC'C -3 ! AvaII,Bme18I,Eco47I,SinI,VpaK11BI >
+;Psp5II 2 rG'GwC_Cy 3 ! PpuMI,PspPPI >F
+;Psp6I 0 'CCwGG_ 5 ! EcoRII,AjnI,BseBI,BstNI,BstOI,Bst2UI,MvaI,PspGI >I
+;Psp1406I 2 AA'CG_TT 2 ! AclI >FK
+;Psp124BI 5 G_AGCT'C -4 ! SacI,Ecl136II,EcoICRI,SstI >IV
+;PspCI 3 CAC'GTG 0 ! PmaCI,AcvI,BbrPI,Eco72I,PmlI >IV
+;PspEI 1 G'GTnAC_C 5 ! BstEII,BstPI,Eco91I,EcoO65I >IV
+PspGI 0 'CCwGG_ 5 ! EcoRII,AjnI,BseBI,BstNI,BstOI,Bst2UI,MvaI,Psp6I >N
+;PspLI 1 C'GTAC_G 4 ! BsiWI,Pfl23II >I
+;PspN4I 3 GGn'nCC 0 ! NlaIV,BmiI,BspLI >I
+PspOMI 1 G'GGCC_C 4 ! ApaI,Bsp120I >INV
+;PspPPI 2 rG'GwC_Cy 3 ! PpuMI,Psp5II >I
+PspXI 2 vC'TCGA_Gb 4 ! >IN
+PsrI 25 GAACnnnnnnTACnnnnnnn_nnnnn' -5 ! >I
+PsrI 25 GTAnnnnnnGTTCnnnnnnn_nnnnn' -5 ! >I
+;PssI 5 rG_GnC'Cy -3 ! DraII,EcoO109I >
+PstI 5 C_TGCA'G -4 ! BspMAI >ABCFGHIJKMNOQRSUVWXY
+;PsuI 1 r'GATC_y 4 ! XhoII,BstX2I,BstYI,MflI >F
+;PsyI 4 GACn'n_nGTC 1 ! Tth111I,AspI,PflFI >F
+PvuI 4 CG_AT'CG -2 ! BpvUI,MvrI,Ple19I >ABFGKMNOQRSUWXY
+PvuII 3 CAG'CTG 0 ! >ABCFGHIJKMNORSUVWXY
+;RcaI 1 T'CATG_A 4 ! BspHI,PagI >M
+;RgaI 5 GCG_AT'CGC -2 ! SgfI,AsiSI >I
+;RigI 6 GG_CCGG'CC -4 ! FseI >I
+;RleAI 18 CCCACAnnnnnnnnn_nnn' -3 ! >
+RsaI 2 GT'AC 0 ! AfaI,Csp6I,CviQI,RsaNI >BCFGHIJMNOQRSVWXY
+;RsaNI 1 G'TA_C 2 ! RsaI,AfaI,Csp6I,CviQI >I
+;RseI 5 CAynn'nnrTG 0 ! MslI,SmiMI >F
+RsrII 2 CG'GwC_CG 3 ! CpoI,CspI,Rsr2I >MNQX
+;Rsr2I 2 CG'GwC_CG 3 ! RsrII,CpoI,CspI >IV
+SacI 5 G_AGCT'C -4 ! Ecl136II,EcoICRI,Psp124BI,SstI >AFGHJKMNOQRSUWX
+SacII 4 CC_GC'GG -2 ! Cfr42I,KspI,Sfr303I,SgrBI,SstII >AGHJKNOQRWX
+SalI 1 G'TCGA_C 4 ! >ABCFGHIJKMNOQRSUVWXY
+SanDI 2 GG'GwC_CC 3 ! >E
+SapI 8 GCTCTTCn'nnn_ 3 ! BspQI,LguI,PciSI >N
+;SatI 2 GC'n_GC 1 ! Fnu4HI,Fsp4HI,ItaI >F
+;SauI 2 CC'TnA_GG 3 ! AxyI,Bse21I,Bsu36I,Eco81I >
+Sau96I 1 G'GnC_C 3 ! AspS9I,BmgT120I,Cfr13I >GJMNOUW
+;Sau3AI 0 'GATC_ 4 ! MboI,BfuCI,Bsp143I,BssMI,BstKTI,BstMBI,DpnII,Kzo9I,NdeII >AGHJKMNOQRSUWX
+SbfI 6 CC_TGCA'GG -4 ! Sse8387I,SdaI >INV
+ScaI 3 AGT'ACT 0 ! AssI,BmcAI,ZrmI >ABCFGJKMNOQRSWX
+;SchI 10 GAGTCnnnnn' 0 ! PleI,MlyI,PpsI >F
+;SciI 3 CTC'GAG 0 ! XhoI,PaeR7I,Sfr274I,SlaI,StrI,TliI >
+ScrFI 2 CC'n_GG 1 ! Bme1390I,BmrFI,BssKI,BstSCI,MspR9I,StyD4I >JMNOS
+;SdaI 6 CC_TGCA'GG -4 ! Sse8387I,SbfI >F
+;SduI 5 G_dGCh'C -4 ! Bsp1286I,MhlI >F
+;SecI 1 C'CnnG_G 4 ! BsaJI,BseDI,BssECI >
+;SelI 0 'CGCG_ 4 ! AccII,Bsh1236I,BspFNI,BstFNI,BstUI,MvnI >
+SetI 4 _AssT' -4 ! >I
+SexAI 1 A'CCwGG_T 5 ! MabI >MN
+SfaNI 10 GCATCnnnnn'nnnn_ 4 ! LweI >INV
+SfcI 1 C'TryA_G 4 ! BfmI,BstSFI >N
+;SfeI 1 C'TryA_G 4 ! BfmI,BstSFI,SfcI >
+SfiI 8 GGCCn_nnn'nGGCC -3 ! >ACFGIJKMNOQRSUVWX
+SfoI 3 GGC'GCC 0 ! NarI,BbeI,DinI,EgeI,EheI,KasI,Mly113I >N
+;Sfr274I 1 C'TCGA_G 4 ! XhoI,PaeR7I,SlaI,StrI,TliI >IV
+;Sfr303I 4 CC_GC'GG -2 ! SacII,Cfr42I,KspI,SgrBI,SstII >IV
+;SfuI 2 TT'CG_AA 2 ! Bpu14I,Bsp119I,BspT104I,BstBI,Csp45I,NspV >M
+;SgfI 5 GCG_AT'CGC -2 ! AsiSI,RgaI >R
+SgrAI 2 Cr'CCGG_yG 4 ! >MN
+;SgrBI 4 CC_GC'GG -2 ! SacII,Cfr42I,KspI,Sfr303I,SstII >C
+SgrDI 2 CG'TCGA_CG 4 ! >F
+;SgsI 2 GG'CGCG_CC 4 ! AscI,PalAI >F
+;SimI 2 GG'GTC_ 3 ! >
+;SinI 1 G'GwC_C 3 ! AvaII,Bme18I,Eco47I,VpaK11BI >GQRWX
+;SlaI 1 C'TCGA_G 4 ! XhoI,PaeR7I,Sfr274I,StrI,TliI >C
+SmaI 3 CCC'GGG 0 ! Cfr9I,TspMI,XmaI,XmaCI >ABCFGHIJKMNOQRSUVWXY
+;SmiI 4 ATTT'AAAT 0 ! SwaI >FIKV
+;SmiMI 5 CAynn'nnrTG 0 ! MslI,RseI >IV
+SmlI 1 C'TyrA_G 4 ! SmoI >N
+;SmoI 1 C'TyrA_G 4 ! SmlI >F
+;SmuI 9 CCCGCnnnn'nn_ 2 ! FauI >F
+;SnaI 3 GTATAC 0 ? ! BssNAI,Bst1107I,BstZ17I >
+SnaBI 3 TAC'GTA 0 ! BstSNI,Eco105I >ACKMNR
+SpeI 1 A'CTAG_T 4 ! AhlI,BcuI >ABGHJKMNOQRSUWX
+SphI 5 G_CATG'C -4 ! BbuI,PaeI >ABCGHIJKMNOQRSVWX
+;SplI 1 C'GTAC_G 4 ! BsiWI,Pfl23II,PspLI >
+SrfI 4 GCCC'GGGC 0 ! >EO
+;Sse9I 0 'AATT_ 4 ! TspEI,TasI,Tsp509I >IV
+;Sse232I 2 CG'CCGG_CG 4 ! MreI >
+;Sse8387I 6 CC_TGCA'GG -4 ! SbfI,SdaI >AK
+;Sse8647I 2 AG'GwC_CT 3 ! >
+;SseBI 3 AGG'CCT 0 ! StuI,AatI,Eco147I,PceI >C
+;SsiI 1 C'CG_C 2 ! AciI,BspACI >F
+SspI 3 AAT'ATT 0 ! >ABCFGIJKMNOQRSUVWX
+;SspD5I 13 GGTGAnnnnnnnn' 0 ! HphI,AsuHPI >
+;SstI 5 G_AGCT'C -4 ! SacI,Ecl136II,EcoICRI,Psp124BI >BC
+;SstII 4 CC_GC'GG -2 ! SacII,Cfr42I,KspI,Sfr303I,SgrBI >B
+;Sth132I 8 CCCGnnnn'nnnn_ 4 ! >
+;Sth302II 2 CC'GG 0 ! HpaII,BsiSI,HapII,MspI >
+;StrI 1 C'TCGA_G 4 ! XhoI,PaeR7I,Sfr274I,SlaI,TliI >U
+;StsI 15 GGATGnnnnnnnnnn'nnnn_ 4 ! FokI,BseGI,BstF5I,BtsCI >
+StuI 3 AGG'CCT 0 ! AatI,Eco147I,PceI,SseBI >ABJKMNQRSUX
+StyI 1 C'CwwG_G 4 ! BssT1I,Eco130I,EcoT14I,ErhI >CJMNRS
+StyD4I 0 'CCnGG_ 5 ! ScrFI,Bme1390I,BmrFI,BssKI,BstSCI,MspR9I >N
+SwaI 4 ATTT'AAAT 0 ! SmiI >GJMNSW
+;TaaI 3 AC_n'GT -1 ! Bst4CI,HpyCH4III >F
+TaiI 4 _ACGT' -4 ! MaeII,HpyCH4IV >F
+TaqI 1 T'CG_A 2 ! >ABCFGIJKMNOQRSUVWXY
+TaqII 17 GACCGAnnnnnnnnn_nn' -2 ! >QX
+TaqII 17 CACCCAnnnnnnnnn_nn' -2 ! >QX
+;TasI 0 'AATT_ 4 ! TspEI,Sse9I,Tsp509I >F
+TatI 1 w'GTAC_w 4 ! >F
+TauI 4 G_CsG'C -3 ! >F
+TfiI 1 G'AwT_C 3 ! PfeI >N
+;TliI 1 C'TCGA_G 4 ! XhoI,PaeR7I,Sfr274I,SlaI,StrI >N
+;Tru1I 1 T'TA_A 2 ! MseI,Tru9I >F
+;Tru9I 1 T'TA_A 2 ! MseI,Tru1I >GIMRVW
+TseI 1 G'CwG_C 3 ! ApeKI >N
+TsoI 17 TArCCAnnnnnnnnn_nn' -2 ! >F
+Tsp45I 0 'GTsAC_ 5 ! NmuCI >N
+Tsp509I 0 'AATT_ 4 ! TspEI,Sse9I,TasI >N
+;Tsp4CI 3 AC_n'GT -1 ! Bst4CI,HpyCH4III,TaaI >
+TspDTI 16 ATGAAnnnnnnnnn_nn' -2 ! >X
+;TspEI 0 'AATT_ 4 ! Sse9I,TasI,Tsp509I >O
+TspGWI 16 ACGGAnnnnnnnnn_nn' -2 ! >X
+;TspMI 1 C'CCGG_G 4 ! SmaI,Cfr9I,XmaI,XmaCI >N
+TspRI 9 _nnCAsTGnn' -9 ! >N
+;TssI 4 GAGnnnCTC 0 ? ! >
+TstI 24 CACnnnnnnTCCnnnnnnn_nnnnn' -5 ! >F
+TstI 25 GGAnnnnnnGTGnnnnnnnn_nnnnn' -5 ! >F
+;TsuI 2 GCGAC 0 ? ! >
+Tth111I 4 GACn'n_nGTC 1 ! AspI,PflFI,PsyI >GIKNQRVWX
+;Tth111II 17 CAArCAnnnnnnnnn_nn' -2 ! >
+;UbaF9I 6 TACnnnnnrTGT 0 ? ! >
+;UbaF11I 2 TCGTA 0 ? ! >
+;UbaF12I 5 CTACnnnGTC 0 ? ! >
+;UbaF13I 6 GAGnnnnnnCTGG 0 ? ! >
+;UbaF14I 5 CCAnnnnnTCG 0 ? ! >
+;UbaPI 3 CGAACG 0 ? ! >
+;UnbI 0 'GGnCC_ 5 ! AspS9I,BmgT120I,Cfr13I,Sau96I >
+;Van91I 7 CCAn_nnn'nTGG -3 ! PflMI,AccB7I,BasI >AFKM
+;Vha464I 1 C'TTAA_G 4 ! AflII,BfrI,BspTI,Bst98I,MspCI >IV
+;VneI 1 G'TGCA_C 4 ! ApaLI,Alw44I >IV
+;VpaK11AI 0 'GGwCC_ 5 ! AvaII,Bme18I,Eco47I,SinI,VpaK11BI >
+;VpaK11BI 1 G'GwC_C 3 ! AvaII,Bme18I,Eco47I,SinI >K
+;VspI 2 AT'TA_AT 2 ! AseI,PshBI >FIRV
+;XagI 5 CCTnn'n_nnAGG 1 ! EcoNI,BstENI >F
+;XapI 1 r'AATT_y 4 ! ApoI,AcsI >F
+XbaI 1 T'CTAG_A 4 ! >ABCFGHIJKMNOQRSUVWXY
+;XceI 5 r_CATG'y -4 ! NspI,BstNSI >F
+XcmI 8 CCAnnnn_n'nnnnTGG -1 ! >N
+XhoI 1 C'TCGA_G 4 ! PaeR7I,Sfr274I,SlaI,StrI,TliI >ABFGHJKMNOQRSUWXY
+;XhoII 1 r'GATC_y 4 ! BstX2I,BstYI,MflI,PsuI >GMRW
+XmaI 1 C'CCGG_G 4 ! SmaI,Cfr9I,TspMI,XmaCI >INRUV
+;XmaIII 1 C'GGCC_G 4 ! BseX3I,BstZI,EagI,EclXI,Eco52I >
+;XmaCI 1 C'CCGG_G 4 ! SmaI,Cfr9I,TspMI,XmaI >M
+;XmaJI 1 C'CTAG_G 4 ! AvrII,AspA2I,BlnI >F
+;XmiI 2 GT'mk_AC 2 ! AccI,FblI >F
+XmnI 5 GAAnn'nnTTC 0 ! Asp700I,MroXI,PdmI >GNRUW
+;XspI 1 C'TA_G 2 ! MaeI,BfaI,FspBI >K
+ZraI 3 GAC'GTC 0 ! AatII >INV
+;ZrmI 3 AGT'ACT 0 ! ScaI,AssI,BmcAI >I
+;Zsp2I 5 A_TGCA'T -4 ! EcoT22I,Mph1103I,NsiI >IV
+
diff --git a/sci-biology/perlprimer/perlprimer-1.1.14.ebuild b/sci-biology/perlprimer/perlprimer-1.1.14.ebuild
new file mode 100644
index 000000000..2b2c5e9a0
--- /dev/null
+++ b/sci-biology/perlprimer/perlprimer-1.1.14.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A GUI application written in Perl to help design
+primers for standard PCR, bisulphite PCR and Real-time PCR"
+HOMEPAGE="http://perlprimer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="dev-perl/perl-tk
+ dev-perl/libwww-perl"
+
+src_unpack() {
+
+ unpack ${A}
+ cd "${S}"
+ sed -i -e "s|\(\"\$HOME\".\"gcg.*\"\)|\"\/usr\/share\/${P}\/\".\"gcg.*\"|" perlprimer.pl || die "Sed failed!"
+}
+
+# TODO: figure out why right-clicking on the sequence doesn't produce a stable menu.
+# see if upstream still exists, point them at the new gcg file.
+
+src_install() {
+
+ exeinto /usr/bin
+ doexe "${S}"/perlprimer.pl
+ insinto /usr/share/${P}
+ doins ${FILESDIR}/gcg.801
+ dodoc Changelog ReadMe.txt
+ dohtml -r tutorial_files tutorial.html
+}
diff --git a/sci-biology/phrap/ChangeLog b/sci-biology/phrap/ChangeLog
new file mode 100644
index 000000000..ad24df867
--- /dev/null
+++ b/sci-biology/phrap/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/phrap
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +phrap-0.990329.ebuild:
+ Mass import from sunrise
+
+ 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +phrap-0.990329.ebuild,
+ +metadata.xml:
+ new package (bug 114094)
+
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
new file mode 100644
index 000000000..72be6ed83
--- /dev/null
+++ b/sci-biology/phrap/Manifest
@@ -0,0 +1,4 @@
+DIST phrap-distrib.tar.Z 366163 RMD160 f6d15059903868b907df225b9022b47957f4004a SHA1 69d9343d1d3bc7edcab2ebca222370fc9db7b9f7 SHA256 e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc
+EBUILD phrap-0.990329.ebuild 864 RMD160 8b68c2d90e42141a40be209940becdaa49905a86 SHA1 2d932bf847b0caf4b29bdd070a3b45bf6667b59d SHA256 4a45b1a66fee1b89b5ef05ab43e64302092c84fba3860459a4224fd7ed92c51b
+MISC ChangeLog 349 RMD160 df3f1863d3b262b9e132f56cca3ef29c32abec3a SHA1 fab185ba0db30f7e38348a51c320e18a07bfd3c5 SHA256 7f9bdafcf31c81b9645bbbe686713674401db183400afc50fe7645e362a0b0e6
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/phrap/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/phrap/phrap-0.990329.ebuild b/sci-biology/phrap/phrap-0.990329.ebuild
new file mode 100644
index 000000000..06cffa641
--- /dev/null
+++ b/sci-biology/phrap/phrap-0.990329.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="Phrap, swat, cross_match: Shotgun assembly and alignment utilities"
+HOMEPAGE="http://www.phrap.org/"
+SRC_URI="phrap-distrib.tar.Z"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
+ einfo '"distrib.tar.Z", then rename it to "phrap-distrib.tar.Z" and put it in'
+ einfo "${DISTDIR}"
+}
+
+src_compile() {
+ sed -i 's/CFLAGS=/#CFLAGS=/' makefile
+ sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' phrapview
+ emake || die "emake failed"
+}
+
+src_install() {
+ dobin cluster cross_match loco phrap phrapview swat
+ for i in {general,phrap,swat}.doc ; do
+ newdoc ${i} ${i}.txt
+ done
+}
diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog
new file mode 100644
index 000000000..7ca249fa6
--- /dev/null
+++ b/sci-biology/proda/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/proda
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild:
+ Mass import from sunrise
+
+ 22 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild, +metadata.xml:
+ new package (bug 175524)
+
diff --git a/sci-biology/proda/Manifest b/sci-biology/proda/Manifest
new file mode 100644
index 000000000..a08c08aed
--- /dev/null
+++ b/sci-biology/proda/Manifest
@@ -0,0 +1,4 @@
+DIST proda_1_0.tar.gz 38868 RMD160 b024496c935cebb74d50479d8cdeacce820358b1 SHA1 44303e1639b5c52278758d23d149ef1c434593a4 SHA256 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08
+EBUILD proda-1.0.ebuild 703 RMD160 46c755309e2925f3ebcc6ede718cd7b3d38c8469 SHA1 e9c55e5782f00660795cb8749c5373f4c1124bbd SHA256 8c454b35cafb73ca9c77662f922cff590498d39dafca97bbf2a4803e8d8c6524
+MISC ChangeLog 335 RMD160 913d0c1816d44d2b575580909498c0ab71a2d16c SHA1 0d4cb7d8379e35695dc9f76df4d6120bd1d7cbbc SHA256 c9a0ed83283201f9dc4e644e83668eb162f6be98cf08e9b55c3df4748355c85d
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/proda/metadata.xml b/sci-biology/proda/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/proda/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/proda/proda-1.0.ebuild b/sci-biology/proda/proda-1.0.ebuild
new file mode 100644
index 000000000..f38a59413
--- /dev/null
+++ b/sci-biology/proda/proda-1.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '_')
+
+DESCRIPTION="Multiple alignment of protein sequences with repeated and shuffled elements"
+HOMEPAGE="http://proda.stanford.edu/"
+SRC_URI="http://proda.stanford.edu/proda_${MY_PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+ unpack ${A}
+ sed -i -e 's/^\(CXXFLAGS =\)/#\1/' \
+ -e 's/#CXXFLAGS = \(-O3.*$(OTHERFLAGS) -funroll-loops\)/CXXFLAGS := ${CXXFLAGS} \1/' \
+ "${S}/Makefile" || die "sed failed"
+}
+
+src_install() {
+ dobin proda
+}
diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog
new file mode 100644
index 000000000..6314ec8cb
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/repeatmasker-libraries
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +repeatmasker-libraries-20061006.ebuild:
+ Mass import from sunrise
+
+ 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +repeatmasker-libraries-20061006.ebuild, +metadata.xml:
+ new package (bug 114096)
+
diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest
new file mode 100644
index 000000000..9fe112592
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/Manifest
@@ -0,0 +1,4 @@
+DIST repeatmaskerlibraries-20061006.tar.gz 5673785 RMD160 ea08ba4dfd49462b92ea9c6ffe64777ec67144d0 SHA1 5cb34e5c9a968f7e6b4a38c642856827469b857c SHA256 a3813d6e1960954f739ec3bb97cf56e9de4e238e420c28caf13c62cbbe247c4b
+EBUILD repeatmasker-libraries-20061006.ebuild 732 RMD160 dee404c6e4f28821b214c4d9900ff700681d9d02 SHA1 df3b98700d4a123cbdfdcdd458a7349ba2e33e26 SHA256 07726f54d11b2d51a951f4af72bce3cd0e9c4d2b64db1ad801640fa3772b4bee
+MISC ChangeLog 400 RMD160 a7b967a97f44050f6aecf9b38cdb5b92153840a9 SHA1 d0acfd86dca1bd200621949093c8487155fb2f62 SHA256 65b876add1d030a87ba29b8aba86bf7ced4e3aa90b100a6b79bf9241e2b9cbcf
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild
new file mode 100644
index 000000000..6e1d528ce
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A special version of RepBase used by RepeatMasker"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/Libraries"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz"
+ einfo 'at http://www.girinst.org/'
+ einfo '(select the "Repbase Update - RepeatMasker edition" link)'
+ einfo 'and place it in '${DISTDIR}
+}
+
+src_install() {
+ dodir /usr/share/repeatmasker/Libraries
+ insinto /usr/share/repeatmasker/Libraries
+ doins "${S}/"*
+}
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
new file mode 100644
index 000000000..1c7082d50
--- /dev/null
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/repeatmasker
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +repeatmasker-3.1.7.ebuild:
+ Mass import from sunrise
+
+ 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +repeatmasker-3.1.7.ebuild,
+ +metadata.xml:
+ new package (bug 114096)
+
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
new file mode 100644
index 000000000..23b9c0245
--- /dev/null
+++ b/sci-biology/repeatmasker/Manifest
@@ -0,0 +1,4 @@
+DIST RepeatMasker-open-3-1-7.tar.gz 8197799 RMD160 fda43f7e3ebe3dbf655b3071e93e6d47fdb8f1e3 SHA1 f36f09f2d4173437ac5eb090ea471b95fdfa832b SHA256 56c2866f7e489e5f606872ff97b509ae29e2b8816b8fd2ad0938edb7c6f788b8
+EBUILD repeatmasker-3.1.7.ebuild 1257 RMD160 dbc84c1ae3d41eaaf785199a665a12b0485053d4 SHA1 e3eb4f37c5683863702f11e18219e72fe3859bed SHA256 e8aca73edea668ad3a5f44ede1402fa65b6c1e5116572189c391a50850c6ae2c
+MISC ChangeLog 364 RMD160 e1877e532b0e93379bc19763efdf5b7358257cc9 SHA1 28c87840dc383e8b463c91888b644b2084398ea3 SHA256 179cbb0e848c489075df2c00191e97c5b9bf1cb55b564548a958c2ab2c063584
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild b/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild
new file mode 100644
index 000000000..d3ff1ce82
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="sci-biology/phrap
+ sci-biology/repeatmasker-libraries"
+
+S="${WORKDIR}/RepeatMasker"
+
+src_compile() {
+ sed -i 's/system( "clear" );//' "${S}/configure"
+ cat << END | "${S}/configure" || die "configure failed"
+
+/usr/bin
+/usr/share/${PN}
+1
+/usr/bin
+Y
+4
+END
+ sed -i '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' "${S}/RepeatMaskerConfig.pm" || die "sed failed"
+ sed -i 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker} || die "sed failed"
+}
+
+src_install() {
+ dobin DateRepeats ProcessRepeats RepeatMasker
+
+ dodir /usr/share/${PN}/lib
+ insinto /usr/share/${PN}/lib
+ doins "${S}"/*.pm
+
+ insinto /usr/share/${PN}
+ doins -r util Matrices
+ keepdir /usr/share/${PN}/Libraries
+
+ dodoc README INSTALL repeatmasker.help daterepeats.help
+}
diff --git a/sci-biology/sibsim4/ChangeLog b/sci-biology/sibsim4/ChangeLog
new file mode 100644
index 000000000..83fc95f4a
--- /dev/null
+++ b/sci-biology/sibsim4/ChangeLog
@@ -0,0 +1,14 @@
+# ChangeLog for sci-biology/sibsim4
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 11 Sep 2007; weaver <weaver@horizon.ath.cx> +sibsim4-0.15.ebuild:
+ version bump
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +sibsim4-0.14.ebuild:
+ Mass import from sunrise
+
+ 18 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +sibsim4-0.14.ebuild,
+ +metadata.xml:
+ new package (bug 175143)
+
diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest
new file mode 100644
index 000000000..18ca25947
--- /dev/null
+++ b/sci-biology/sibsim4/Manifest
@@ -0,0 +1,6 @@
+DIST SIBsim4-0.14.tar.gz 28956 RMD160 7e54d8973d750d80516c3cc2ce358230e3e8c4cf SHA1 ee4215b191b494074df4fe33088097e00e789393 SHA256 15c0493ddc21cb4086bcc2f72d6e7ac470256cd8d87605de359b59a853fb9596
+DIST SIBsim4-0.15.tar.gz 29090 RMD160 b9c56dd5bc2c69a2eefce7b15aa064d53c5ee8f0 SHA1 c0660daa7b95d986fc08dd6247014bbf3631cdd5 SHA256 d2b9c40d5935f1dc2bd66a65f80a907e0cfa7d317d304090ad32aa28b9f46a1b
+EBUILD sibsim4-0.14.ebuild 542 RMD160 272b1b10dbd5346f28615b60b3293084da1c968e SHA1 3ec8dd7a03def6ffca466ab4cb1c104694708834 SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b
+EBUILD sibsim4-0.15.ebuild 542 RMD160 272b1b10dbd5346f28615b60b3293084da1c968e SHA1 3ec8dd7a03def6ffca466ab4cb1c104694708834 SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b
+MISC ChangeLog 429 RMD160 f0cac89ceeef990602eb76883532e934c0b19851 SHA1 a3a863686f2477f003b3a94aecc01b6b708750f1 SHA256 a99f78b1ab05bb2504312d4f3d0e90b1e64b5573768d8a7a65d2489aebca4ed6
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/sibsim4/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/sibsim4/sibsim4-0.14.ebuild b/sci-biology/sibsim4/sibsim4-0.14.ebuild
new file mode 100644
index 000000000..64ada6178
--- /dev/null
+++ b/sci-biology/sibsim4/sibsim4-0.14.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner"
+HOMEPAGE="http://sibsim4.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/SIBsim4-${PV}"
+
+src_unpack() {
+ unpack ${A}
+ sed -i 's/CFLAGS = \(.*\)/CFLAGS := \1 ${CFLAGS}/' ${S}/Makefile
+}
+
+src_install() {
+ dobin SIBsim4
+ doman SIBsim4.1
+}
diff --git a/sci-biology/sibsim4/sibsim4-0.15.ebuild b/sci-biology/sibsim4/sibsim4-0.15.ebuild
new file mode 100644
index 000000000..64ada6178
--- /dev/null
+++ b/sci-biology/sibsim4/sibsim4-0.15.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner"
+HOMEPAGE="http://sibsim4.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/SIBsim4-${PV}"
+
+src_unpack() {
+ unpack ${A}
+ sed -i 's/CFLAGS = \(.*\)/CFLAGS := \1 ${CFLAGS}/' ${S}/Makefile
+}
+
+src_install() {
+ dobin SIBsim4
+ doman SIBsim4.1
+}
diff --git a/sci-biology/tgi-tools/ChangeLog b/sci-biology/tgi-tools/ChangeLog
new file mode 100644
index 000000000..9c5619c04
--- /dev/null
+++ b/sci-biology/tgi-tools/ChangeLog
@@ -0,0 +1,20 @@
+# ChangeLog for sci-biology/tgi-tools
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tgi-tools-0.1.ebuild:
+ Mass import from sunrise
+
+ 15 Apr 2007; Stefan Schweizer <genstef@gentoo.org> tgi-tools-0.1.ebuild:
+ Remove RESTRICT=mirror, Artistic license allows redistribution
+
+ 14 Dec 2006; Markus Ullmann <jokey@gentoo.org> tgi-tools-0.1.ebuild:
+ Whiteys
+
+ 12 Dec 2006; Jakub Moc <jakub@gentoo.org> tgi-tools-0.1.ebuild:
+ QA: quoting, formatting, nomirror -> mirror etc.
+
+ 12 Dec 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx>
+ +tgi-tools-0.1.ebuild, +metadata.xml:
+ New ebuild, Bug 157827
+
diff --git a/sci-biology/tgi-tools/Manifest b/sci-biology/tgi-tools/Manifest
new file mode 100644
index 000000000..443c95624
--- /dev/null
+++ b/sci-biology/tgi-tools/Manifest
@@ -0,0 +1,14 @@
+DIST cdbfasta.tar.gz 23470 RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e SHA1 c7455ad2ac92cd1ee1293f0100fd871d71e4d630 SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c
+DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d
+DIST nrcl.tar.gz 13151 RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 SHA1 a9bf20a6f0f10201a03fb51644fa64e2519abd84 SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808
+DIST psx.tar.gz 7797 RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 SHA1 3e0ac61f9ef2e546ff571bfc269e904138b445b9 SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a
+DIST pvmsx.tar.gz 10963 RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 SHA1 562ea8628e47739ec7b98c622c894fe45e210c98 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230
+DIST sclust.tar.gz 14370 RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e SHA1 19afe2272cb8b01e631313d57c38cd7fc575fc3c SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4
+DIST seqclean.tar.gz 181383 RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 SHA1 8b3871cc0d70d71ff1bc7bfedc3638ff60e4c889 SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d
+DIST tclust.tar.gz 8864 RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 SHA1 35793ddc161c31ce0827073e993f4f6456dbbd35 SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445
+DIST tgi_cpp_library.tar.gz 58212 RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 SHA1 1039291f5f0ca617d025bcfacf4f271a3a225001 SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875
+DIST trimpoly.tar.gz 12562 RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 SHA1 3558e9663cba6e6c179ca6f9a019f95d7aa1d4db SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f
+DIST zmsort.tar.gz 5537 RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 SHA1 27a88033d99da8671fcae598f21e5b8cb7089e40 SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd
+EBUILD tgi-tools-0.1.ebuild 1556 RMD160 3a3782fd845e309a5a5cef84a870d7529581f684 SHA1 1fb231c11bf653fd7645380cb0c4fbbeb2478f0a SHA256 d5548b8ea3e0600a731e8bf9b186dd4027bcc7422b0960a17e072041e817d15e
+MISC ChangeLog 697 RMD160 d873f6a3192e71e8499646192ef725f58987ba96 SHA1 5f916419a43396c3ecd92b93f1ec732ca4f65999 SHA256 2111f501e89d7be9aa417de1aa13d2163740c3b7284d93c07db3924385e5ed57
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/tgi-tools/metadata.xml b/sci-biology/tgi-tools/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/tgi-tools/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
new file mode 100644
index 000000000..9a50c4bb3
--- /dev/null
+++ b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+
+for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do
+ SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz"
+done
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="pvm"
+KEYWORDS="~x86"
+
+DEPEND="pvm? ( sys-cluster/pvm )"
+RDEPEND=${DEPEND}
+
+S=${WORKDIR}
+
+src_unpack() {
+ unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
+ for i in nrcl sclust tclust zmsort psx pvmsx; do
+ mkdir "${S}"/${i}
+ cd "${S}"/${i}
+ unpack ${i}.tar.gz
+ done
+}
+
+src_compile() {
+ sed -i 's/use Mailer;/#use Mailer;/' ${S}/seqclean/seqclean
+ sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp
+ # TODO: fix error in nrcl
+ for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
+ sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile
+ cd ${S}/${i} || die "cd ${i} failed"
+ emake || die "emake failed in ${i}"
+ done
+}
+
+src_install() {
+ dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
+ for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
+ dobin ${i}/${i}
+ done
+ for i in cdbfasta seqclean; do
+ newdoc ${i}/README README.${i}
+ done
+}
diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog
new file mode 100644
index 000000000..8ac88cca5
--- /dev/null
+++ b/sci-biology/tigr-assembler/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/tigr-assembler
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+ +tigr-assembler-2.0.ebuild:
+ Mass import from sunrise
+
+ 19 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tigr-assembler-2.0.ebuild,
+ +metadata.xml:
+ new package (bug 175282)
+
diff --git a/sci-biology/tigr-assembler/Manifest b/sci-biology/tigr-assembler/Manifest
new file mode 100644
index 000000000..aa4e756b4
--- /dev/null
+++ b/sci-biology/tigr-assembler/Manifest
@@ -0,0 +1,4 @@
+DIST TIGR_Assembler_v2.tar.gz 3252950 RMD160 5b7eaeebf8791acb3b53ab864f6e9c6571c70877 SHA1 8bd1886eb33d203598ac03decc7798a1fa0d85d7 SHA256 b5b660db388788173f7bd9778fe9b1e904bed7f6a464ab6cc92cd4608e70fd42
+EBUILD tigr-assembler-2.0.ebuild 635 RMD160 d899446e7e35320a8a3023d690c45c58b939e062 SHA1 ed6846be95b4b769205fcfa16dfdb4cd4ddb430c SHA256 75cecd058f71fb26541672c951bfeb6461a4e7f021d635ddc377bc83e8cea25c
+MISC ChangeLog 366 RMD160 456390461b0286ece0f75002dcd49f90bd42e754 SHA1 a6d057fde4a594d8fb2d127bbb443d85ea039d9a SHA256 9b8273b2bfb0bd78ef4656523a6edd6e4fc4d4467c90fdc34995c1f95662c288
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/tigr-assembler/metadata.xml b/sci-biology/tigr-assembler/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/tigr-assembler/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild
new file mode 100644
index 000000000..bc42ce0b6
--- /dev/null
+++ b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A whole-genome shotgun assembler from TIGR"
+HOMEPAGE="http://www.tigr.org/software/assembler/"
+SRC_URI="ftp://ftp.tigr.org/pub/software/assembler/TIGR_Assembler_v2.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/TIGR_Assembler_v2"
+
+src_compile() {
+ sed -i 's/CFLAGS.*= -O/CFLAGS := -O ${CFLAGS}/' "${S}/src/Makefile" || die "sed failed"
+ cd "${S}/src"
+ emake || die "emake failed"
+}
+
+src_install() {
+ dobin bin/{run_TA,TIGR_Assembler}
+ dodoc README
+}
diff --git a/sci-chemistry/gtk-gamess/ChangeLog b/sci-chemistry/gtk-gamess/ChangeLog
new file mode 100644
index 000000000..cd09f4e50
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/gtk-gamess
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 08 Oct 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+ Adding ~amd64. For amd64 users, manually installing gamess
+ is still your responsibility at this point.
+
+ 04 Jan 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+ Initial gtk-gamess ebuild.
+
diff --git a/sci-chemistry/gtk-gamess/Manifest b/sci-chemistry/gtk-gamess/Manifest
new file mode 100644
index 000000000..efe1b994d
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/Manifest
@@ -0,0 +1,4 @@
+DIST gtk-gamess-2.00.tar.gz 174125 RMD160 6c57d9222027bdd533980a8bcc138491ce6c8e28 SHA1 66dfddeb756a0cb683815502da3f29ce812a4fdc SHA256 f282cdb94ddccba196b2ea0964cc2c26e3a4db5c8ac3b9f51d72a5a0e45f9e0e
+EBUILD gtk-gamess-2.00.ebuild 594 RMD160 5df43c62d33afd2cf3c96d9bb80d7627cb3110e7 SHA1 2025a75c77efba6fff716099cb341689189ca477 SHA256 6c20e4e5e393b010020fe0d69b5cad52b1c0566c846fdbd8b645eeb52be33a0f
+MISC ChangeLog 381 RMD160 910bc4fdead96f99e04dbfd1479cf7fedda22265 SHA1 e9e8fe875f794d6b12a128fb8ebb716ef20ba454 SHA256 c7d80827512e999b2ddf360738e233e0ef680ad5fc1b7845cf030157289e6f3b
+MISC metadata.xml 392 RMD160 2d06a6dd8c2e049f9f9994ef8e08d7fd1bbf96b2 SHA1 c4b76377f98397b277c82ced30a9a839901a5e69 SHA256 48aab8e6edc81adc6436c92cc90a65d169e909ec03e6999b1788a14f5dbc7cc1
diff --git a/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild b/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild
new file mode 100644
index 000000000..79ffca971
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="GTK-GAMESS is a graphical frontend for GAMESS, a General Atomic and Molecular Electronic Structure System"
+HOMEPAGE="http://sourceforge.net/projects/gtk-gamess/"
+
+SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+
+KEYWORDS="~amd64 x86"
+
+IUSE=""
+
+RDEPEND=">=gnome-base/libglade-2.4
+ >=x11-libs/gtk+-2.6
+ dev-libs/libxml2
+ sci-chemistry/gamess"
+
+src_install() {
+
+ make DESTDIR="${D}" install || die "install failed"
+ dodoc README
+}
diff --git a/sci-chemistry/gtk-gamess/metadata.xml b/sci-chemistry/gtk-gamess/metadata.xml
new file mode 100644
index 000000000..141e5e93f
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>je_fro@gentoo.org</email>
+<name>Jeff Gardner</name>
+</maintainer>
+<longdescription lang="en">
+gtk-gamess is a frontend to GAMESS that allows users to queue and run quantum
+chemistry calculations.
+</longdescription>
+</pkgmetadata>
+
diff --git a/sci-electronics/gerbv/ChangeLog b/sci-electronics/gerbv/ChangeLog
new file mode 100644
index 000000000..b7d6288b7
--- /dev/null
+++ b/sci-electronics/gerbv/ChangeLog
@@ -0,0 +1,83 @@
+# ChangeLog for sci-electronics/gerbv
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-electronics/gerbv/ChangeLog,v 1.13 2006/07/23 22:05:37 tsunam Exp $
+
+*gerbv-1.0.2 (03 Aug 2006)
+
+ 03 Aug 2006; Lucas Chiesa <lucas.chiesa@gmail.com> gerbv-1.0.2.ebuild:
+ Added new ebuild for 1.0.2.
+
+ 23 Jul 2006; Joshua Jackson <tsunam@gentoo.org> gerbv-1.0.1-r1.ebuild:
+ Stable x86; bug #141421
+
+ 23 Jul 2006; Tobias Scherbaum <dertobi123@gentoo.org>
+ gerbv-1.0.1-r1.ebuild:
+ ppc stable, bug #141421
+
+ 02 Jul 2006; Denis Dupeyron <calchan@gentoo.org> metadata.xml:
+ Adjusted metadata, see bug #138062.
+
+ 13 Mar 2006; Scott Stoddard <deltacow@gentoo.org> gerbv-1.0.1-r1.ebuild:
+ Added ~amd64.
+
+ 10 Mar 2006; <plasmaroo@gentoo.org> gerbv-1.0.1-r1.ebuild,
+ +files/gerbv-1.0.0-gcc-4.10.patch:
+ Fix GCC4 compile issue (bug #125186).
+
+ 22 Jan 2006; <plasmaroo@gentoo.org> gerbv-0.15.ebuild, gerbv-0.16-r1.ebuild,
+ -gerbv-0.16.ebuild, gerbv-1.0.1-r1.ebuild, -gerbv-1.0.1.ebuild:
+ Port to modular X; clear up stale ebuilds.
+
+*gerbv-1.0.1-r1 (01 Oct 2005)
+*gerbv-0.16-r1 (01 Oct 2005)
+
+ 01 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +gerbv-0.16-r1.ebuild,
+ +gerbv-1.0.1-r1.ebuild:
+ Removing deprecated "gtk2" USE flag (bug #106560).
+
+ 17 May 2005; Michael Hanselmann <hansmi@gentoo.org> gerbv-0.15.ebuild:
+ Stable on ppc.
+
+*gerbv-1.0.1 (13 Mar 2005)
+
+ 13 Mar 2005; <plasmaroo@gentoo.org> -gerbv-1.0.0.ebuild,
+ +gerbv-1.0.1.ebuild:
+ Version bump; bug #83007.
+
+ 18 Feb 2005; Michael Hanselmann <hansmi@gentoo.org> gerbv-1.0.0.ebuild:
+ Added to ~ppc.
+
+*gerbv-1.0.0 (02 Jan 2005)
+
+ 02 Jan 2005; <plasmaroo@gentoo.org> +gerbv-1.0.0.ebuild,
+ +files/gerbv-1.0.0-Xinerama.patch:
+ Version bump.
+
+*gerbv-0.16 (27 Dec 2004)
+
+ 27 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+ +gerbv-0.15.ebuild, +gerbv-0.16.ebuild:
+ Moved from app-sci/gerbv to sci-electronics/gerbv.
+
+ 23 Oct 2004; <plasmaroo@gentoo.org> gerbv-0.15.ebuild:
+ Added "media-libs/gdk-pixbuf" dependency; bug #67304.
+
+*gerbv-0.16 (24 Jun 2004)
+
+ 24 Jun 2004; <plasmaroo@gentoo.org> +gerbv-0.16.ebuild:
+ Version bump.
+
+ 05 Jun 2004; David Holm <dholm@gentoo.org> gerbv-0.15.ebuild:
+ Added to ~ppc.
+
+ 19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> gerbv-0.15.ebuild:
+ Removed S, added IUSE
+
+ 30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>; gerbv-0.15.ebuild:
+ Change x11-base/xfree dependency to virtual/x11.
+
+*gerbv-0.15 (27 Nov 2003)
+
+ 27 Nov 2003; <plasmaroo@gentoo.org> gerbv-0.15.ebuild:
+ Initial import.
+
diff --git a/sci-electronics/gerbv/Manifest b/sci-electronics/gerbv/Manifest
new file mode 100644
index 000000000..1316ff776
--- /dev/null
+++ b/sci-electronics/gerbv/Manifest
@@ -0,0 +1,5 @@
+AUX gerbv-1.0.0-Xinerama.patch 1484 RMD160 0cd65704d2c458424c259c40026d9140a96e4e52 SHA1 8c3dfe7343a83708ece91b9f5bad036a2267ca31 SHA256 db0e17a39e3f8852453cd31000173fc9e3454c7bfa02cff3bcf5bfe8cdd75079
+DIST gerbv-1.0.2.tar.gz 1066247 RMD160 f5d7e00fd9576f6ed8d0f1dee457fc9dd2c98c26 SHA1 4ed3bd604eaf6bbefc868f3eb6e379d28ecc0f84 SHA256 87ec664cc5b161047d017f0ca9fbb5de9e428186f010c1f869ecd0a6384e0e7d
+EBUILD gerbv-1.0.2.ebuild 1012 RMD160 b30597b8edb23485dfd57aa1042c0073c1291f54 SHA1 864d806f040d6c6336e880cee3159343c0dd86a3 SHA256 5bfe25fa99847dc1228f9464f8ee8cd9a580869571712f3a8a5be7fde6b16c7b
+MISC ChangeLog 2576 RMD160 2439ea25264684ed87c602df0915928ec2cb7e89 SHA1 5e692f4f2139983ef6bbabe3ca1beab2cbb7ccc2 SHA256 cf8d0f799ac7ee9b83ede9cf85c99c660d50a1e5334ea41e3f9bffd92ed7a03e
+MISC metadata.xml 414 RMD160 0801ddc4c2838d5fdc7ceae7454035fc373d2877 SHA1 b91b7436fc30f9a340fcd030dcc5a809843c03ea SHA256 437f367a7dd127a77d7f0e4880e29ce42b36d6eb2bde9e318142ac45f530851d
diff --git a/sci-electronics/gerbv/files/gerbv-1.0.0-Xinerama.patch b/sci-electronics/gerbv/files/gerbv-1.0.0-Xinerama.patch
new file mode 100644
index 000000000..40e296b8c
--- /dev/null
+++ b/sci-electronics/gerbv/files/gerbv-1.0.0-Xinerama.patch
@@ -0,0 +1,44 @@
+diff -ur gerbv-1.0.0/ChangeLog gerbv-1.0.0.new/ChangeLog
+--- gerbv-1.0.0/ChangeLog 2004-12-27 23:31:10.000000000 +0000
++++ gerbv-1.0.0.new/ChangeLog 2005-01-02 01:54:21.074734456 +0000
+@@ -269,6 +269,10 @@
+ * src/gerber.c: Doesn't warn anymore if a gerber file requests an
+ image rotate on zero degrees. Reported by Balaji V.
+
++2003-03-03 Jeffrey W. Baker <jwbaker@acm.org>
++
++ * src/gerbv.c: fix initial window size for multihead systems.
++
+ 2003-03-02 Stefan Petersen <spe@stacken.kth.se>
+
+ * src/draw_amacro.c: Aperture macro primitive 1 is a filled circle.
+diff -ur gerbv-1.0.0/src/gerbv.c gerbv-1.0.0.new/src/gerbv.c
+--- gerbv-1.0.0/src/gerbv.c 2004-09-24 20:12:25.000000000 +0100
++++ gerbv-1.0.0.new/src/gerbv.c 2005-01-02 01:53:21.241830440 +0000
+@@ -2485,7 +2485,7 @@
+ GtkWidget *hbox;
+ GtkWidget *menubar;
+ GtkStyle *textStyle;
+- gint screen_width, width, height;
++ gint width, height;
+ int read_opt;
+ int i;
+ int req_width = -1, req_height = -1, req_x = 0, req_y = 0;
+@@ -2611,9 +2610,14 @@
+ width = req_width;
+ height = req_height;
+ } else {
+- screen_width = gdk_screen_width();
+- width = screen_width * 3/4;
+- height = width * 3/4;
++ GdkScreen *screen;
++ int nmonitors;
++
++ screen = gdk_screen_get_default();
++ nmonitors = gdk_screen_get_n_monitors(screen);
++
++ width = gdk_screen_get_width(screen) * 3/4 / nmonitors;
++ height = gdk_screen_get_height(screen) * 3/4 / nmonitors;
+ }
+
+ /*
diff --git a/sci-electronics/gerbv/gerbv-1.0.2.ebuild b/sci-electronics/gerbv/gerbv-1.0.2.ebuild
new file mode 100644
index 000000000..c5bc53e6d
--- /dev/null
+++ b/sci-electronics/gerbv/gerbv-1.0.2.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-electronics/gerbv/gerbv-1.0.1-r1.ebuild,v 1.6 2006/07/23 22:05:37 tsunam Exp $
+
+inherit eutils
+
+DESCRIPTION="gerbv - The gEDA Gerber Viewer"
+SRC_URI="http://www.geda.seul.org/dist/${P}.tar.gz"
+HOMEPAGE="http://www.geda.seul.org"
+
+IUSE="doc png xinerama"
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="=x11-libs/gtk+-2*
+ png? ( media-libs/libpng
+ media-libs/gdk-pixbuf )"
+
+src_compile() {
+ local confOptions
+
+ confOptions='--enable-gtk2'
+ use xinerama && epatch ${FILESDIR}/${PN}-1.0.0-Xinerama.patch
+ use png || confOptions="$confOptions --disable-exportpng"
+
+ econf $confOptions || die
+ emake || die
+}
+
+src_install () {
+ make DESTDIR=${D} install || die
+ dodoc AUTHORS COPYING ChangeLog NEWS README TODO
+ if use doc; then
+ cd doc
+ dodoc sources.txt
+ use png && dodoc PNG-print/PNGPrintMiniHowto.txt
+ docinto eagle
+ dodoc eagle/eagle2exc*
+ fi
+}
diff --git a/sci-electronics/gerbv/metadata.xml b/sci-electronics/gerbv/metadata.xml
new file mode 100644
index 000000000..80893f75d
--- /dev/null
+++ b/sci-electronics/gerbv/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-electronics</herd>
+ <longdescription>
+ Gerber Viewer (gerbv) is a viewer for Gerber files. The standard supported by
+ gerbv is RS-274X. gerbv also supports drill files. The format supported are
+ known under names as NC-drill or Excellon.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-electronics/gsmc/ChangeLog b/sci-electronics/gsmc/ChangeLog
new file mode 100644
index 000000000..4935e3795
--- /dev/null
+++ b/sci-electronics/gsmc/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-electronics/gsmc
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 23 Oct 2005; Lucas Chiesa <lucas.chiesa@gmail.com> gsmc-1.0.ebuild:
+ Changed ${PN}-${PV} to ${P}. It now depends on >=x11-libs/gkt+-2.6.8.
+ Removed PREFIX=/usr/ from the make install line.
+
+*gsmc-1.0 (23 Oct 2005)
+
+ 23 Oct 2005; Lucas Chiesa <lucas.chiesa@gmail.com> gsmc-1.0.ebuild:
+ Initial import of gsmc - A program for doing Smith Chart calculations.
diff --git a/sci-electronics/gsmc/Manifest b/sci-electronics/gsmc/Manifest
new file mode 100644
index 000000000..1bce96513
--- /dev/null
+++ b/sci-electronics/gsmc/Manifest
@@ -0,0 +1,4 @@
+DIST gsmc-1.0.tar.gz 77095 RMD160 ac0f89204a5e450d6e3675be9ea81846680d6d30 SHA1 cc46769c39511d08c81a1c37590c8f89d5e61f32 SHA256 59386860b15d921375f2a254c92f0264dee23642d66fb864fea4940471690c59
+EBUILD gsmc-1.0.ebuild 557 RMD160 3029c263e520f8a59c0f7679de9b306be1f82e47 SHA1 aaef2777dd359a3376d03c1b1e412184e633fa71 SHA256 d99c9925f804c6dd31cdb73d224edb32a26d0e5eec2f342f6c8cf60c442961fb
+MISC ChangeLog 483 RMD160 4c652163bd09de7957d8d8601de03c147e424cc8 SHA1 e3701e077e2dabcba453d851433475c8d40f1386 SHA256 3b5c38e78cc97a60a151e1b85e13a3435a052b059139bd2723ec5ad632b4a1f9
+MISC metadata.xml 253 RMD160 a980be058c9a5aee8bee00e48c38ef728155a038 SHA1 176bcb0c5ee8f51bf2a1dd312fc5677993fa9211 SHA256 40e278af9ee48e5fcdef1a7b8b988c17c55bbcbf6f5e6c3bbc4c8ee833f6b055
diff --git a/sci-electronics/gsmc/gsmc-1.0.ebuild b/sci-electronics/gsmc/gsmc-1.0.ebuild
new file mode 100644
index 000000000..3c8aae490
--- /dev/null
+++ b/sci-electronics/gsmc/gsmc-1.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="A GTK program for doing Smith Chart calculations"
+HOMEPAGE="http://www.qsl.net/ik5nax/"
+SRC_URI="http://www.qsl.net/ik5nax/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/gtk+-2.6.8"
+RDEPEND=""
+
+src_compile() {
+ econf || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ make DESTDIR=${D} install || die "make install failed"
+ dodoc AUTHORS NEWS README ChangeLog TODO
+}
diff --git a/sci-electronics/gsmc/metadata.xml b/sci-electronics/gsmc/metadata.xml
new file mode 100644
index 000000000..06a199400
--- /dev/null
+++ b/sci-electronics/gsmc/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+ <email> lucas.chiesa@gmail.com </email>
+ <name> Lucas Chiesa </name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-electronics/linsmith/ChangeLog b/sci-electronics/linsmith/ChangeLog
new file mode 100644
index 000000000..cd013f628
--- /dev/null
+++ b/sci-electronics/linsmith/ChangeLog
@@ -0,0 +1,48 @@
+# ChangeLog for sci-electronics/linsmith
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*linsmith-0.99.1 (15 Jul 2006)
+
+ 15 Jul 2006; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.99.1.ebuild:
+ Version bump. Removed previous versions.
+
+*linsmith-0.9.8 (06 Jul 2006)
+
+ 06 Jul 2006; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.8.ebuild:
+ Version bump. Removed previous versions.
+
+ 14 Apr 2006; Marcus D. Hanwell <cryos@gentoo.org> linsmith-0.9.5.ebuild:
+ Various small cleanups of the ebuild, added examples USE flag and marked
+ ~amd64.
+
+*linsmith-0.9.5 (14 Apr 2006)
+
+ 14 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.5.ebuild:
+ Version bump.
+
+*linsmith-0.9.4 (09 Apr 2006)
+
+ 09 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.4.ebuild:
+ Version bump. Fixed bug which prevented the documentation from being
+ installed when USE="doc" was used. Removed previous versions.
+
+*linsmith-0.9.2 (16 Nov 2005)
+
+ 16 Nov 2005; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.2.ebuild:
+ Added ebuild for linsmith 0.9.2. Removed lyx dependency as the documentation
+ is now distributed in pdf. Added desktop and icon file.
+
+*linsmith-0.9.1 (3 Nov 2005)
+
+ 3 Nov 2005; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.1.ebuild:
+ Added doc use flag which compiles a lyx manual included in the source.
+ Patch Makefile.am to prevent it installing examples in /usr/share/linsmith.
+ Added the man page from the debian package.
+
+*linsmith-0.9.0_alpha3 (25 Oct 2005)
+
+ 23 Oct 2005; Lucas Chiesa <lucas.chiesa@gmail.com> linsmith-0.9.0_alpha3:
+ Initial import of lismith - Smith Charting program, mainly designed for
+ educational use. Thanks to Vincent Paeder <vpaeder@net2000.ch> for the initial
+ ebuild. Closes bug #79082.
diff --git a/sci-electronics/linsmith/Manifest b/sci-electronics/linsmith/Manifest
new file mode 100644
index 000000000..48aab741a
--- /dev/null
+++ b/sci-electronics/linsmith/Manifest
@@ -0,0 +1,5 @@
+AUX linsmith-datafiles.patch 757 RMD160 61cbef351c36677c6a894e3c017c1f57a5724b00 SHA1 54a13968f2593868d483fc221899141f95b61f8d SHA256 b39d2ece3aac52e0bfe35010c436771aa9fa623f2508f290d36e40853fe979ce
+DIST linsmith-0.99.1.tar.gz 949495 RMD160 abfd52f666bdd41959883160fcd8c16c1f398302 SHA1 b892b3dfdc4ea5575fc132fca32e5ff1b4ecef48 SHA256 5f58d0419f77be3b9f8e308dda3844121f0b6498e9cdd8f91ba72214a780b3b7
+EBUILD linsmith-0.99.1.ebuild 1437 RMD160 27722c1753caeac6eab30c7e61f6d7b78dffa105 SHA1 122d3002ad8d61dd45fb5f788a64e993403cc4e4 SHA256 9938543742745fdaae8f71ca6f2ce133e08a0f492b7b8eacf10c51b3c0d5a001
+MISC ChangeLog 1810 RMD160 30f98154ce8ebf59d3407f4aacc8800d7d738743 SHA1 6f4b49a54f89440a0c8d9d5ca69a971341d2d32d SHA256 958f30994e4c89fd5d694eed230f01aed969f00f9d71e97130095fee3d555d36
+MISC metadata.xml 272 RMD160 c1308e7326e25dcbbd93cebf0e45e230909a73cd SHA1 e94b2b237bd541fa1e9ccfd44ce303b4d29efee0 SHA256 ed4065c0dd146c683a3c9a21e3f021d3764696faa99abd43919ebd16d8fb9bed
diff --git a/sci-electronics/linsmith/files/linsmith-datafiles.patch b/sci-electronics/linsmith/files/linsmith-datafiles.patch
new file mode 100644
index 000000000..cae7a2a7c
--- /dev/null
+++ b/sci-electronics/linsmith/files/linsmith-datafiles.patch
@@ -0,0 +1,30 @@
+--- Makefile.am.old 2005-11-03 00:56:51.000000000 -0300
++++ Makefile.am 2005-11-03 00:57:09.000000000 -0300
+@@ -20,15 +20,6 @@
+ fi \
+ done \
+ fi
+- @$(NORMAL_INSTALL)
+- if test -d $(srcdir)/datafiles; then \
+- $(mkinstalldirs) $(DESTDIR)$(datadir)/$(PACKAGE); \
+- for datafile in $(srcdir)/datafiles/*; do \
+- if test -f $$datafile; then \
+- $(INSTALL_DATA) $$datafile $(DESTDIR)$(datadir)/$(PACKAGE); \
+- fi \
+- done \
+- fi
+
+ dist-hook:
+ if test -d pixmaps; then \
+@@ -39,11 +30,3 @@
+ fi \
+ done \
+ fi
+- if test -d datafiles; then \
+- mkdir $(distdir)/datafiles; \
+- for datafile in datafiles/*; do \
+- if test -f $$datafile; then \
+- cp -p $$datafile $(distdir)/datafiles; \
+- fi \
+- done \
+- fi
diff --git a/sci-electronics/linsmith/linsmith-0.99.1.ebuild b/sci-electronics/linsmith/linsmith-0.99.1.ebuild
new file mode 100644
index 000000000..a986fa744
--- /dev/null
+++ b/sci-electronics/linsmith/linsmith-0.99.1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils
+
+DESCRIPTION="linSmith is a Smith Charting program, mainly designed for educational use"
+HOMEPAGE="http://jcoppens.com/soft/linsmith/index.en.php"
+SRC_URI="mirror://sourceforge/linsmith/${P}.tar.gz"
+
+LICENSE="GPL-2 LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples"
+
+DEPEND=">=gnome-base/libgnomeprint-2.10.3
+ >=dev-libs/libxml2-2.6.20-r2
+ >=gnome-base/libgnomeui-2.10.1"
+RDEPEND=""
+
+src_unpack() {
+ unpack ${A}
+ cd ${S}
+ # This patch is to prevent make install copying
+ # the examples in /usr/share/linsmith
+ # Now they are cp to the correct location.
+ epatch ${FILESDIR}/${PN}-datafiles.patch
+
+ einfo "Regenerating autotools files..."
+ WANT_AUTOMAKE=1.9 automake || die "automake failed"
+}
+
+src_install() {
+ # Delete this file, otherwise it is installed with the pixmaps.
+ rm pixmaps/Makefile.am~
+
+ make DESTDIR=${D} install || die "make install failed"
+
+ insinto "/usr/share/${PN}"
+ doins datafiles/conv0809
+
+ dodoc AUTHORS NEWS README ChangeLog TODO
+ doman doc/linsmith.1
+
+ insinto "/usr/share/applications"
+ doins linsmith.desktop
+ insinto "/usr/share/pixmaps/${PN}"
+ doins linsmith_icon.xpm
+
+ if use doc; then
+ insinto "/usr/share/doc/${PF}"
+ doins doc/manual.pdf
+ fi
+
+ if use examples; then
+ insinto "/usr/share/doc/${PF}/examples"
+ doins datafiles/*.circ datafiles/*.load
+ fi
+}
diff --git a/sci-electronics/linsmith/metadata.xml b/sci-electronics/linsmith/metadata.xml
new file mode 100644
index 000000000..14a9e8c57
--- /dev/null
+++ b/sci-electronics/linsmith/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-electronics</herd>
+<maintainer>
+ <email> lucas.chiesa@gmail.com </email>
+ <name> Lucas Chiesa </name>
+</maintainer>
+</pkgmetadata>
+
diff --git a/sci-electronics/player/ChangeLog b/sci-electronics/player/ChangeLog
new file mode 100644
index 000000000..328300801
--- /dev/null
+++ b/sci-electronics/player/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-electronics/player
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*player-2.0.4 (23 Nov 2007)
+
+ 23 Nov 2007; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
+ +player-2.0.4.ebuild:
+ Initial import. Thanks Angelo Arrifano for his work. See bug #26373 for
+ problems.
diff --git a/sci-electronics/player/Manifest b/sci-electronics/player/Manifest
new file mode 100644
index 000000000..4771113a6
--- /dev/null
+++ b/sci-electronics/player/Manifest
@@ -0,0 +1,16 @@
+DIST player-2.0.4.tar.bz2 1707996 RMD160 8b70fef48595afcf9fafe24cf57f7a3fa9ba8628 SHA1 96ae46abe9a81cab045b2a9ae6479a44fc6f2ac2 SHA256 615225f22e0585df2a5fdf9adaddbe6e2a9ca25f1015607f51a47023fcc2cdf9
+EBUILD player-2.0.4.ebuild 3244 RMD160 c68f0fd9e50cbd636b58d05fa945f126c384a708 SHA1 72073dc8517d8a7b31eeb41926da8f610c18a61f SHA256 bb60c8f25c68c8506bec7c37561bd91c8e341b504383c69e6c5c722ff9edc958
+MD5 97e0cf7807d853fe91c6f895bacdee75 player-2.0.4.ebuild 3244
+RMD160 c68f0fd9e50cbd636b58d05fa945f126c384a708 player-2.0.4.ebuild 3244
+SHA256 bb60c8f25c68c8506bec7c37561bd91c8e341b504383c69e6c5c722ff9edc958 player-2.0.4.ebuild 3244
+MISC ChangeLog 333 RMD160 c786b271eb3246ae32d5f2d9e772e2c684c4e16b SHA1 ffc46959673005cdef733ac16f72aadfda6d474c SHA256 bbd5fab9039f953a798d6aeb9020a23742dc757a9848950127ab3d53580e7e6a
+MD5 87f026f26522d11a8c600015148c5f54 ChangeLog 333
+RMD160 c786b271eb3246ae32d5f2d9e772e2c684c4e16b ChangeLog 333
+SHA256 bbd5fab9039f953a798d6aeb9020a23742dc757a9848950127ab3d53580e7e6a ChangeLog 333
+MISC metadata.xml 169 RMD160 c200fa2c4703eb26cf6ba49efb830c4f23678a5b SHA1 f97e1ffdd53446fb93f5b6b1225099c45337b0b4 SHA256 0b291e8666ec5ca169baa47793c8865f2f930efd84136d69b9010770a910930a
+MD5 a04562cf03638eee3bbb927891b05c31 metadata.xml 169
+RMD160 c200fa2c4703eb26cf6ba49efb830c4f23678a5b metadata.xml 169
+SHA256 0b291e8666ec5ca169baa47793c8865f2f930efd84136d69b9010770a910930a metadata.xml 169
+MD5 c5638b65b4c96da69d4f3a395efa6da1 files/digest-player-2.0.4 244
+RMD160 b9cbc7de0f912aa4ac4d4c2bf8f11692014070d1 files/digest-player-2.0.4 244
+SHA256 fa632a9a05d205683f94c5a1ecbbfb020077e61b6c1dc6744da2e2a31016fe74 files/digest-player-2.0.4 244
diff --git a/sci-electronics/player/metadata.xml b/sci-electronics/player/metadata.xml
new file mode 100644
index 000000000..aa78ded2d
--- /dev/null
+++ b/sci-electronics/player/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-electronics</herd>
+</pkgmetadata>
+
diff --git a/sci-electronics/player/player-2.0.4.ebuild b/sci-electronics/player/player-2.0.4.ebuild
new file mode 100644
index 000000000..481abf347
--- /dev/null
+++ b/sci-electronics/player/player-2.0.4.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils
+
+DESCRIPTION="A network server for robot control"
+HOMEPAGE="http://playerstage.sourceforge.net/index.php?src=player"
+SRC_URI="mirror://sourceforge/playerstage/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+
+#DRIVERS NOT INCLUDED
+# nd - unknown
+# passthrough - unknown
+# artoolkitplus - needs arToolKitPlus (not in portage)
+# garcia - needs Garcia (not in portage)
+# imageseq - needs openCV (not in portage)
+# shapetracker - needs openCV (not in portage)
+# simpleshape - needs openCV (not in portage)
+# upcbarcode - needs openCV (not in portage)
+# isense - needs iSense (not in portage)
+# nomad - needs Creative Nomad (maybe in portage)
+# yarpimage - needs YarpCam (not in portage)
+# rcore_xbridge - needs libparticle (not in portage)
+
+IUSE="ieee1394 sphinx2 wifi v4l test
+ boost gnome gtk openssl festival
+ opengl glut gsl java python doc"
+
+RDEPEND="media-libs/jpeg
+ opengl? ( virtual/opengl )
+ glut? ( virtual/glut )
+ openssl? ( dev-libs/openssl )
+ imagemagick? ( media-gfx/imagemagick )
+ gsl? ( sci-libs/gsl )
+ python? ( dev-lang/python )
+ ieee1394? ( sys-libs/libraw1394 media-libs/libdc1394 )
+ java? ( virtual/jdk dev-lang/python )
+ gtk? ( x11-libs/gtk+ )
+ gnome? ( >=gnome-base/libgnomecanvas-2.0 )
+ boost? ( dev-libs/boost )
+ sphinx2? ( app-accessibility/sphinx2 )
+ festival? ( app-accessibility/festival )"
+
+DEPEND="${RDEPEND}
+ python? ( dev-lang/swig )
+ java? ( dev-lang/swig )
+ doc? ( app-doc/doxygen )"
+
+
+src_compile() {
+ local drivers driver nodep_drivers
+
+ nodep_drivers="acoustics acts amcl amtecpowercube
+ aodv bumpersafe canonvcc4 clodbuster cmucam2
+ cmvision dummy er1 fakelocalize flockofbirds
+ garminnmea iwspy khepera laserbar laserbarcode
+ lasercspace laserposeinterpolator laserrescan
+ lasersafe laservisualbarcode laservisualbw
+ lifomcom linuxjoystick logfile mapcspace
+ microstrain mixer obot p2os erratic wbr914
+ ptu46 reb relay kartowriter rflex segwayrmp
+ service_adv_mdns sicklms200 sicknav200 sickpls
+ sicks3000 highspeedsick sonyevid30 urglaser vfh
+ vmapfile waveaudio roomba wavefront insideM300
+ skyetekM1 mica2 cameracompress"
+
+ for driver in ${NODEP_DRIVERS}; do
+ drivers="${drivers} $(use_enable ${driver})"
+ done
+ drivers="${drivers}
+ $(use_enable sphinx2)
+ $(use_enable gtk mapfile)
+ $(use_enable gtk mapscale)
+ $(use_enable wifi linuxwifi)
+ $(use_enable festival)
+ $(use_enable v4l camerauvc)
+ $(use_enable v4l camerav4l)
+ $(use_enable v4l sphere)
+ $(use_enable ieee1394 camera1394)"
+
+ econf \
+ $(use_enable java jplayer) \
+ $(use_enable openssl md5) \
+ $(use_enable python libplayerc-py) \
+ $(use_enable gtk rtkgui) \
+ $(use_enable test tests) \
+ --with-playercc \
+ ${drivers} || die "econf failed"
+
+ # Parallel make will fail
+ emake -j1 || die "emake failed"
+
+ if use doc; then
+ pushd doc
+ emake doc || die "emake doc failed"
+ popd
+ fi
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+
+ if use doc; then
+ cd doc
+ emake DESTDIR="${D}" "doc-install" || die "emake doc-install failed"
+ cd ..
+ fi
+
+ dodoc AUTHORS ChangeLog NEWS README TODO || die
+}
diff --git a/sci-electronics/stage/ChangeLog b/sci-electronics/stage/ChangeLog
new file mode 100644
index 000000000..fc7658bba
--- /dev/null
+++ b/sci-electronics/stage/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-electronics/player
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*stage-2.0.3 (25 Nov 2007)
+
+ 25 Nov 2007; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
+ +stage-2.0.3.ebuild:
+ Initial import. Thanks Angelo Arrifano for his work. See bug #185298 for
+ problems.
diff --git a/sci-electronics/stage/Manifest b/sci-electronics/stage/Manifest
new file mode 100644
index 000000000..7739a55af
--- /dev/null
+++ b/sci-electronics/stage/Manifest
@@ -0,0 +1,20 @@
+AUX stage-2.0.3-docdst-fix.patch 372 RMD160 0265721b92d0e6a2ef3c7bb31b687318656ee693 SHA1 463065f0b076d729f537b889299b5578812f29f3 SHA256 a0821007072f3d90da900b1f30d3a28fe7989341ed885082a47e7a4f8f591388
+MD5 bcc7b899bc1be0e54c724b6c023cb189 files/stage-2.0.3-docdst-fix.patch 372
+RMD160 0265721b92d0e6a2ef3c7bb31b687318656ee693 files/stage-2.0.3-docdst-fix.patch 372
+SHA256 a0821007072f3d90da900b1f30d3a28fe7989341ed885082a47e7a4f8f591388 files/stage-2.0.3-docdst-fix.patch 372
+DIST stage-2.0.3.tar.bz2 451664 RMD160 4f22d8c423de37d70e099a6593a94ab2f8eaf021 SHA1 2595fa2b004cc81fcdd89d1630bffa55304c7522 SHA256 7a9619f5ef633d18a11900da1e59e807547180fce4420bb9e9b4c681ddbe6c83
+EBUILD stage-2.0.3.ebuild 1238 RMD160 1e14bdc41e38a86044488442c70fd90bf778e76a SHA1 9277c6491b47bd6a2daf4282d2d6ad3271971cfd SHA256 2b6ed7a95d454d322b7da8e841649a354ae34281f47400939a9915d9f5afc94b
+MD5 ce3c823b8656de05263a328aba416f27 stage-2.0.3.ebuild 1238
+RMD160 1e14bdc41e38a86044488442c70fd90bf778e76a stage-2.0.3.ebuild 1238
+SHA256 2b6ed7a95d454d322b7da8e841649a354ae34281f47400939a9915d9f5afc94b stage-2.0.3.ebuild 1238
+MISC ChangeLog 332 RMD160 ac0eb19506e1f4b1a3a697425b23c6453e18fefa SHA1 70a5f4638a329be756a335f42a6ce6045cf2f480 SHA256 94c26682a32bb2aabade20fde9d5baf836329f0c91dde588c5af9f35485c963a
+MD5 d27f239f473133b8661c2ccf42235865 ChangeLog 332
+RMD160 ac0eb19506e1f4b1a3a697425b23c6453e18fefa ChangeLog 332
+SHA256 94c26682a32bb2aabade20fde9d5baf836329f0c91dde588c5af9f35485c963a ChangeLog 332
+MISC metadata.xml 168 RMD160 02ffa2a6bfc173f6a601931fc931eb411d1f1a07 SHA1 caa9701abcacc8b45314ce04b0a8ebc5f04dfc09 SHA256 182df1c85b4fe43ec45658071ebe6cf7f23cc51288ea2e14ea46f7c5b1391e6f
+MD5 0c85a4d253e03ab9ba216b40fbad3f5f metadata.xml 168
+RMD160 02ffa2a6bfc173f6a601931fc931eb411d1f1a07 metadata.xml 168
+SHA256 182df1c85b4fe43ec45658071ebe6cf7f23cc51288ea2e14ea46f7c5b1391e6f metadata.xml 168
+MD5 a0d1ecfa3ae0a2a8393745a6e8924cb3 files/digest-stage-2.0.3 238
+RMD160 ae880e7f6342170797963783edb8b960adafd992 files/digest-stage-2.0.3 238
+SHA256 dafd12547705b9960710e1fd0d614f4c474d480bb54745a66224f8de803b8225 files/digest-stage-2.0.3 238
diff --git a/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch b/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch
new file mode 100644
index 000000000..889a03d22
--- /dev/null
+++ b/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch
@@ -0,0 +1,12 @@
+diff -ur stage-2.0.3/docsrc/Makefile.am stage-2.0.3-fix/docsrc/Makefile.am
+--- stage-2.0.3/docsrc/Makefile.am 2006-06-09 02:39:47.000000000 +0200
++++ stage-2.0.3-fix/docsrc/Makefile.am 2007-07-14 15:06:31.414020298 +0200
+@@ -9,7 +9,7 @@
+
+ #header.html
+
+-DOCDIR = $(prefix)/share/doc
++DOCDIR = $(DESTDIR)$(prefix)/share/doc
+
+ # build docs manually with 'make doc'
+ doc:
diff --git a/sci-electronics/stage/metadata.xml b/sci-electronics/stage/metadata.xml
new file mode 100644
index 000000000..53ae7d77c
--- /dev/null
+++ b/sci-electronics/stage/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-electronics</herd>
+</pkgmetadata>
diff --git a/sci-electronics/stage/stage-2.0.3.ebuild b/sci-electronics/stage/stage-2.0.3.ebuild
new file mode 100644
index 000000000..e14d3f0f2
--- /dev/null
+++ b/sci-electronics/stage/stage-2.0.3.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit autotools eutils
+
+DESCRIPTION="2D multiple-robot simulator."
+HOMEPAGE="http://playerstage.sourceforge.net/index.php?src=stage"
+SRC_URI="mirror://sourceforge/playerstage/stage-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="doc"
+
+RDEPEND=">=x11-libs/gtk+-2.4
+ >=sci-electronics/player-2.0.2
+ x11-apps/rgb"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+
+ epatch "${FILESDIR}"/${P}-docdst-fix.patch
+ sed -i \
+ -e 's;/usr/X11R6/lib/X11/rgb.txt;/usr/share/X11/rgb.txt;' \
+ configure.ac || die "sed failed"
+ eautoreconf
+}
+
+src_compile() {
+ #Disable gnome-canvas since its experimental
+ econf --disable-gnomecanvas || die "econf failed"
+ emake || die "emake failed"
+
+ if use doc; then
+ pushd docsrc
+ doxygen -u stage.dox || die "doxygen failed"
+ touch header.html
+ emake "doc" || die "emake doc failed"
+ popd
+ fi
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+
+ if use doc; then
+ pushd docsrc
+ emake DESTDIR="${D}" "doc-install" || die "emake doc-install failed"
+ popd
+ fi
+
+ dodoc AUTHORS ChangeLog NEWS README || die
+}
diff --git a/sci-libs/cgal-python/Manifest b/sci-libs/cgal-python/Manifest
new file mode 100644
index 000000000..6650be7cc
--- /dev/null
+++ b/sci-libs/cgal-python/Manifest
@@ -0,0 +1,3 @@
+DIST cgal-python-0.9.1.tar.gz 146703 RMD160 e52f352b359678132db3019ed2d5edec57dd93a3 SHA1 38d08c28ac31eb2f84289a7e2487c49b2575b11f SHA256 507608cf34e6bdee77fdc0aaa753a2d882a8e1f36fb2531bc52a44774bc902e1
+EBUILD cgal-python-0.9.1.ebuild 1107 RMD160 5535aa19d07856cf7a17e8d99ead8e5b5dd16cec SHA1 92887ad601aa5a5361a77a7a3756275883bc81dc SHA256 370c1847ff7deb0eed3e5064cc76bbccfb80fde54dc7b2f8c1f258f30a7b963e
+MISC metadata.xml 169 RMD160 e1db75ae5d177dffc400468c7d76a7e1fe41876d SHA1 0c953712f9b97d5ab3f95ae71997ffbc96c4007d SHA256 36837b011d26f0b83477c7a8632cb0099aedbcba5a3e45c61f20292e079f6180
diff --git a/sci-libs/cgal-python/cgal-python-0.9.1.ebuild b/sci-libs/cgal-python/cgal-python-0.9.1.ebuild
new file mode 100644
index 000000000..64ee76434
--- /dev/null
+++ b/sci-libs/cgal-python/cgal-python-0.9.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit python toolchain-funcs
+
+DESCRIPTION="Provide Python bindings for the CGAL library"
+HOMEPAGE="http://cgal-python.gforge.inria.fr/"
+SRC_URI="http://gforge.inria.fr/frs/download.php/945/${P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="examples"
+
+DEPEND="sci-libs/cgal"
+RDEPEND="sci-libs/cgal"
+
+src_unpack(){
+ python_version
+ unpack "${A}"
+ cd "${S}"
+ # include python header needed by boost
+ for i in $(find ./bindings/ -name Makefile); do
+ sed "s:-I../..:-I/usr/include/python${PYVER} -I../..:g" -i $i
+ sed "s:@g++:$(tc-getCXX) -fno-strict-aliasing:g" -i $i
+ done
+}
+
+src_compile(){
+ CGAL_MAKEFILE=/usr/share/CGAL/makefile emake
+}
+
+src_install(){
+ CGAL_MAKEFILE=/usr/share/CGAL/makefile emake package
+ pylibdir="$(${python} -c 'from distutils.sysconfig import get_python_lib;print get_python_lib()')"
+ dodir "${pylibdir}"
+ cp -r cgal_package/CGAL "${D}/${pylibdir}"
+ if use example; then
+ dodir /usr/share/doc/${P}
+ cp -r ./test "${D}/usr/share/doc/${P}"
+ fi
+}
diff --git a/sci-libs/cgal-python/metadata.xml b/sci-libs/cgal-python/metadata.xml
new file mode 100644
index 000000000..3190fbf9c
--- /dev/null
+++ b/sci-libs/cgal-python/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-geosciences</herd>
+</pkgmetadata>
diff --git a/sci-libs/cgal/Manifest b/sci-libs/cgal/Manifest
new file mode 100644
index 000000000..1ed3ce408
--- /dev/null
+++ b/sci-libs/cgal/Manifest
@@ -0,0 +1,5 @@
+AUX cgal_redhat.patch 847 RMD160 e2a34445fc5d4ef3ff700e640ae0c0724cc8b014 SHA1 f68421364555d0f0b1c55f33aee65de94023bb0a SHA256 150b3c57a2031f95e5227628806d5f4bc587cc10f68bc3e7335d374a4db277a5
+AUX cgal_soname.patch 436 RMD160 abbaf339bc91c55cc85688b0d431c73314c37838 SHA1 3a290d1844fa59c4015860931eb772aef698144b SHA256 1d51e828c7c4a13e0d9ba9120a55d09ffde5a35b8b4141827868e0f6805a4ae1
+DIST CGAL-3.2.1.tar.gz 6391058 RMD160 a0d484140c58f19c0aecd2085588df4d51d41165 SHA1 7999cdd99b35324a6cd0c4c1747e08f5bcd87b95 SHA256 b3dd4fa56744738cb77f18c5097a409fa0ab8245e745fb56e8ebca4311c2a353
+EBUILD cgal-3.2.1.ebuild 3640 RMD160 63328ed295a0f90cede55b177bce19b9be33000b SHA1 78fcb2727f174047d074add1458c01e920042a68 SHA256 9c175795ca341598bc2cabf362400a921f455f2a8d180f5d4c16efe0ab97eea3
+MISC metadata.xml 169 RMD160 e1db75ae5d177dffc400468c7d76a7e1fe41876d SHA1 0c953712f9b97d5ab3f95ae71997ffbc96c4007d SHA256 36837b011d26f0b83477c7a8632cb0099aedbcba5a3e45c61f20292e079f6180
diff --git a/sci-libs/cgal/cgal-3.2.1.ebuild b/sci-libs/cgal/cgal-3.2.1.ebuild
new file mode 100644
index 000000000..3c61263ad
--- /dev/null
+++ b/sci-libs/cgal/cgal-3.2.1.ebuild
@@ -0,0 +1,121 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils toolchain-funcs qt3
+
+DESCRIPTION="The Computational Geometry Algorithms Library is an Open
+Source C++ library of geometric algorithms and data structures."
+HOMEPAGE="http://www.cgal.org/"
+DLPAGE="http://www.cgal.org/download/"
+PKN="$(echo ${PN} | tr {a-z} {A-Z})"
+PK="$(echo ${P} | tr {a-z} {A-Z})"
+SRC_URI="${PK}.tar.gz"
+#SRC_URI="ftp://ftp.mpi-sb.mpg.de/pub/outgoing/${PKN}/${PK}.tar.gz"
+
+LICENSE="LGPL-2 QPL"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="X zlib qt3 examples"
+RESTRICT="fetch"
+
+DEPEND="zlib? ( sys-libs/zlib )
+ qt3? ( $(qt_min_version 3.0) )
+ examples? ( $(qt_min_version 3.0) )
+ X? ( virtual/x11 )
+ dev-libs/mpfr
+ sci-libs/libcore
+ dev-libs/gmp
+ dev-libs/boost"
+RDEPEND="virtual/libc"
+
+S="${WORKDIR}/${PK}"
+
+pkg_nofetch() {
+ einfo "Due to license restrictions that may apply to the file in this"
+ einfo "package, you must download ${SRC_URI} file manually from"
+ einfo "${DLPAGE} and put it in ${DISTDIR}."
+}
+
+src_unpack(){
+ if use examples; then
+ ewarn "Examples actualy require 28M of disk space."
+ fi
+ unpack "${A}"
+ cd "${S}"
+ epatch "${FILESDIR}/${PN}_soname.patch"
+ # Patch from redhat bug #199168
+ # http://bugzilla.redhat.com/bugzilla/attachment.cgi?id=135376
+ # it should be not applied becauseof its textrelaction and issue
+ # about undefined symbol: _ZN18QMetaObjectCleanUpC1EPKcPFP11QMetaObjectvE
+ # epatch "${FILESDIR}/${PN}_redhat.patch"
+}
+
+src_compile(){
+ CGALDIR="${S}/cgal_install_dir"
+ myconf="--prefix=${CGALDIR} \
+ --with-boost=n \
+ --with-boost-param-options=n \
+ --with-core=n \
+ --with-gmp=n \
+ --with-gmpxx=n \
+ --with-mpfr=n"
+
+ use X && myconf="${myconf} --with-x11=n"
+ use zlib && myconf="${myconf} --with-zlib=n"
+ if use qt3 || use examples; then
+ myconf="${myconf} --with-qt3mt=n --qt_incl_dir ${QTDIR}/include/ \
+ --qt_lib_dir ${QTDIR}/lib"
+ fi
+
+ myconf="${myconf} --without-autofind"
+
+ # we use CORE headers provided by libcore
+ rm -r "${S}/include/CORE"
+
+ ./install_cgal ${myconf} -ni $(which $(tc-getCXX)) || \
+ die "Unable to compile"
+}
+
+src_install(){
+ SDIR="$(ls ${CGALDIR}/lib/)"
+ LIBNAME="${CGALDIR}/lib/${SDIR}/libCGAL"
+
+ dolib "${LIBNAME}.a" "${LIBNAME}.so" || die "Unable to install ${LIBNAME}"
+ if use qt3 || use examples; then
+ dolib "${LIBNAME}Qt.a" ||\
+ die "Unable to install ${LIBNAME}Qt.a"
+ #"${LIBNAME}Qt.so"
+ fi
+ dosym "/usr/lib/libCGAL.so" "/usr/lib/libCGAL.so.1" && \
+ dosym "/usr/lib/libCGAL.so" "/usr/lib/libCGAL.so.1.0.0" || \
+ die "Unable to create symlinks"
+
+ CGALINC="${CGALDIR}/include/"
+ rm -r "${CGALINC}/OpenNL/LICENSE.OPENNL" || \
+ die "Unable to remove uneeded headers"
+ if ! use qt3 || ! use examples ; then
+ rm $(find ${CGALINC}/CGAL/ -name "Qt*") || \
+ die "Unable to remove Qt headers"
+ fi
+ cp -rp "${CGALINC}" "${D}/usr/" || \
+ die "Unable to install headers"
+
+ sed "s:${CGALDIR}:/usr:g" -i \
+ "${CGALDIR}/make/makefile_${SDIR}" || die "Unable to correct makefle"
+ dodir "/usr/share/CGAL" || die "Unable to create share directory"
+ cp "${CGALDIR}/make/makefile_${SDIR}" "${D}/usr/share/CGAL/makefile" || \
+ die "Unable to install makefile"
+ einfo "CGAL_MAKEFILE was installed in : /usr/share/CGAL/makefile"
+
+ if use examples; then
+ dodir /usr/share/doc/${P}
+ cp -r "${S}/demo" "${D}/usr/share/doc/${P}"
+ cp -r "${S}/examples" "${D}/usr/share/doc/${P}"
+ einfo "There are 2 directories : demo and examples in"
+ einfo "/usr/share/doc/${P}"
+ einfo "which contains samples applications. To compile them"
+ einfo "use the following command :"
+ einfo "CGAL_MAKEFILE=/usr/share/CGAL/makefile make"
+ fi
+}
diff --git a/sci-libs/cgal/files/cgal_redhat.patch b/sci-libs/cgal/files/cgal_redhat.patch
new file mode 100644
index 000000000..77a4073e1
--- /dev/null
+++ b/sci-libs/cgal/files/cgal_redhat.patch
@@ -0,0 +1,27 @@
+diff -ur src/CGALQt/makefile src/CGALQt/makefile
+--- src/CGALQt/makefile 2006-05-23 17:15:58.000000000 +0200
++++ src/CGALQt/makefile 2006-05-24 15:59:33.000000000 +0200
+@@ -71,15 +71,21 @@
+
+ static_lib: lib
+
+-lib: lib_no_install
++lib: lib_no_install lib_shared
+ mv $(CGAL_QT_LIB) $(CGAL_LIB_DESTINATION)
++ mv libCGALQt.so $(CGAL_LIB_DESTINATION)
++ rm $(CGAL_OBJECTS)
+
+ lib_no_install: $(CGAL_OBJECTS)
+ $(CGAL_LIB_CREATE)$(CGAL_QT_LIB) \
+ `ls *$(OBJ_EXT) | awk '{for (i=1; i<=NF;++i){printf "$(CGAL_OBJ_PREFIX)";print $$i}}'`\
+ $(CGAL_LIB_LDFLAGS)
+ $(RANLIB) $(CGAL_QT_LIB)
+- rm $(CGAL_OBJECTS)
++
++lib_shared: $(CGAL_OBJECTS)
++ $(CGAL_SHARED_LIB_CREATE)libCGALQt.so \
++ `ls *$(OBJ_EXT) | awk '{for (i=1; i<=NF;++i){printf "$(CGAL_OBJ_PREFIX)";print $$i}}'`\
++ $(CGAL_LIB_LDFLAGS)
+
+ clean:
+ rm -f $(CGAL_QT_LIB) $(CGAL_OBJECTS) *.moc
diff --git a/sci-libs/cgal/files/cgal_soname.patch b/sci-libs/cgal/files/cgal_soname.patch
new file mode 100644
index 000000000..a0bfb630d
--- /dev/null
+++ b/sci-libs/cgal/files/cgal_soname.patch
@@ -0,0 +1,11 @@
+--- install_cgal 2006-07-13 21:01:01.000000000 +0200
++++ install_cgal 2006-10-04 13:33:18.000000000 +0200
+@@ -767,7 +767,7 @@
+ CGAL_OBJ_PREFIX=""
+ CGAL_SHARED_LIB_CXXFLAGS="-fpic"
+ CGAL_SHARED_LIB_LDFLAGS=
+- CGAL_SHARED_LIB_CREATE="\$(CGAL_CXX) -shared"
++ CGAL_SHARED_LIB_CREATE="\$(CGAL_CXX) -shared -Wl,-soname,libCGAL.so.1"
+ CGAL_SHARED_LIB_INSTALL_NAME=""
+ CGAL_WINLIB_CXXFLAGS=""
+ CGAL_QT_CXXFLAGS=""
diff --git a/sci-libs/cgal/metadata.xml b/sci-libs/cgal/metadata.xml
new file mode 100644
index 000000000..3190fbf9c
--- /dev/null
+++ b/sci-libs/cgal/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-geosciences</herd>
+</pkgmetadata>
diff --git a/sci-libs/jama/ChangeLog b/sci-libs/jama/ChangeLog
new file mode 100644
index 000000000..b23a774a4
--- /dev/null
+++ b/sci-libs/jama/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-libs/jama
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 17 Dec 2007; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
+ +jama-1.2.5.ebuild:
+ Initial import
+
diff --git a/sci-libs/jama/Manifest b/sci-libs/jama/Manifest
new file mode 100644
index 000000000..973ca3b66
--- /dev/null
+++ b/sci-libs/jama/Manifest
@@ -0,0 +1,5 @@
+DIST jama102doc.zip 61085 RMD160 c68377da88b1dc300e39b3eeabda730d5647307b SHA1 40fbbfd6faa17956d6211c27bdf6660b837b3a9c SHA256 0175a981cba82b316f17e1066e605a1bc6aa2840edf70b5e1a06305f16e5f7e3
+DIST jama125.zip 16277 RMD160 e36476e35245235f09905ae5518adaaabb59c188 SHA1 5ca8b154d0a0c30e2c50700ffe70567315ebcf2c SHA256 7432bf51d7101f63d5880421f940f64cea124f1460ff2fcfb6226e6744d1360c
+EBUILD jama-1.2.5.ebuild 626 RMD160 9f2f532aa7835644fcf5a96169bf073c39afaf9d SHA1 a4b648d62db6a1b6f3530a0bad97b48d41314a76 SHA256 182a6aae9c734cc056c9492d3b339f01a4d35a4e87ea7b9ce3d13666e3218731
+MISC ChangeLog 224 RMD160 06e81f6675c9eb7713d59f8ec234a943c97dfed3 SHA1 552ae50fd534d16b21fe6fa45aa945c90e5571ae SHA256 b70263c913b018148d10978ec249bc06d23e3201cb8a13b148142b5676afb0ea
+MISC metadata.xml 472 RMD160 1c0426134e50e9803ff8317e047b17e37b3295a4 SHA1 7961e2f2081aef2954cc4ea2283a8700af6cfd96 SHA256 368b7be799007fdaf744a75987f9f34716c5386d86856cd7c19540d2ca0959d0
diff --git a/sci-libs/jama/jama-1.2.5.ebuild b/sci-libs/jama/jama-1.2.5.ebuild
new file mode 100644
index 000000000..e126b794c
--- /dev/null
+++ b/sci-libs/jama/jama-1.2.5.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils
+
+MYPV=${PV//./}
+DOCPV=102
+
+DESCRIPTION="Java-like matrix C++ templates"
+HOMEPAGE="http://math.nist.gov/tnt/"
+SRC_URI="http://math.nist.gov/tnt/${PN}${MYPV}.zip
+ doc? ( http://math.nist.gov/tnt/${PN}${DOCPV}doc.zip )"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="doc"
+
+DEPEND="app-arch/unzip"
+RDEPEND="sci-libs/tnt"
+
+S="${WORKDIR}"
+
+src_compile() {
+ einfo "Nothing to compile"
+}
+
+src_install() {
+ insinto /usr/include
+ doins *.h || die
+ use doc && dohtml doxygen/html/*
+}
diff --git a/sci-libs/jama/metadata.xml b/sci-libs/jama/metadata.xml
new file mode 100644
index 000000000..6b12ce442
--- /dev/null
+++ b/sci-libs/jama/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+JAMA/C++: a translation of the Java Matrix Library, developed by the
+Mathworks and NIST, into C++ . It includes the following routines:
+* classical matrix linear algebra
+* QR
+* SVD
+* Cholesky
+* Eigenvalue solver
+It is based on NIST's Template Numerical Toolkit.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/lapackpp/ChangeLog b/sci-libs/lapackpp/ChangeLog
new file mode 100644
index 000000000..0ad3c5d2d
--- /dev/null
+++ b/sci-libs/lapackpp/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-libs/lapackpp
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 20 Aug 2007; Sébastien Fabbro <bicatali@gentoo.org>
+ +lapackpp-2.5.2.ebuild, +metadata.xml:
+ Initial import
+
diff --git a/sci-libs/lapackpp/Manifest b/sci-libs/lapackpp/Manifest
new file mode 100644
index 000000000..c3985bd5d
--- /dev/null
+++ b/sci-libs/lapackpp/Manifest
@@ -0,0 +1,4 @@
+DIST lapackpp-2.5.2.tar.gz 571096 RMD160 4afe2d18d78450b8ad11ed350b597a2eab09ad38 SHA1 24a5867cf5cea4c3505597beb85121f71a342561 SHA256 f79c985801e1de9d8b5165894c60fd3b08818e9b0a406ff29fe48783a5134a9c
+EBUILD lapackpp-2.5.2.ebuild 880 RMD160 a5380e010266bfb732f49cc31f2bdb9f8d90d075 SHA1 2ea1ddda89a0282cb9cdc0981a1ef2eec97b5ed6 SHA256 59558a056a86d829d80aa2bae9b6c68f252cd51c22beb41b88910a473b033f72
+MISC ChangeLog 232 RMD160 ff2edbb4039e144655f8660d53849b8a4cc543a7 SHA1 44c84bc527ef81be0b34dc71c440d2d66dafb04a SHA256 c09db4778ce957cfdc5c5eb956cc22580198a0bcdb674119c097e4280de9add4
+MISC metadata.xml 843 RMD160 6ae5c4725768374a0d9b1b511230693c2056e005 SHA1 74da47532a68ad6a64e515d8793c7e4d08fda448 SHA256 91ec444b6dd8603a84b473e8272d4b7b0c10bd6641b12506627fcf86cecf4ed8
diff --git a/sci-libs/lapackpp/lapackpp-2.5.2.ebuild b/sci-libs/lapackpp/lapackpp-2.5.2.ebuild
new file mode 100644
index 000000000..7446b1229
--- /dev/null
+++ b/sci-libs/lapackpp/lapackpp-2.5.2.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="C++ wrapper for LAPACK"
+HOMEPAGE="http://lapackpp.sourceforge.net"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+LICENSE="LGPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+RDEPEND="virtual/blas
+ virtual/lapack"
+DEPEND="${DEPEND}
+ dev-util/pkgconfig
+ doc? ( app-doc/doxygen )"
+
+src_compile() {
+ econf \
+ --disable-atlas \
+ --with-blas="$(pkg-config --libs blas)" \
+ --with-lapack="$(pkg-config --libs lapack)" \
+ || die "econf failed"
+ emake || die "emake failed"
+ if use doc; then
+ emake srcdoc || die "emake srcdoc failed"
+ fi
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc NEWS README ChangeLog AUTHORS || die "dodoc failed"
+ if use doc; then
+ dohtml api-doc/html || die "dohtml failed"
+ fi
+}
diff --git a/sci-libs/lapackpp/metadata.xml b/sci-libs/lapackpp/metadata.xml
new file mode 100644
index 000000000..96625413a
--- /dev/null
+++ b/sci-libs/lapackpp/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+LAPACK++ (Linear Algebra PACKage in C++) is a software library for
+numerical linear algebra that solves systems of linear equations and eigenvalue
+problems on high performance computer architectures.
+
+Computational support is provided for supports various matrix classes
+for vectors, non-symmetric matrices, SPD matrices, symmetric matrices,
+banded, triangular, and tridiagonal matrices; however, it does not include all
+of the capabilities of original f77 LAPACK. Emphasis is given to
+routines for solving linear systems consisting of non-symmetric matrices,
+symmetric positive definite systems, and solving linear least-square
+systems.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/matio/ChangeLog b/sci-libs/matio/ChangeLog
new file mode 100644
index 000000000..2e51a3bb3
--- /dev/null
+++ b/sci-libs/matio/ChangeLog
@@ -0,0 +1,21 @@
+# ChangeLog for sci-libs/matio
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*matio-1.3.1 (20 Sep 2006)
+
+ 20 Sep 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +matio-1.3.1.ebuild, -matio-1.3.0.ebuild, -files/matio-1.1.4.patch:
+ version bump, now at sourceforge
+
+*matio-1.3.0 (28 August 2006)
+
+ 28 August 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +matio-1.3.0.ebuild, -matio-1.1.4.ebuild:
+ version bump
+
+*matio-1.1.4 (16 June 2006)
+
+ 16 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su>
+ +metadata.xml, +matio-1.1.4.ebuild, +files/matio-1.1.4.patch:
+ Initial import.
diff --git a/sci-libs/matio/Manifest b/sci-libs/matio/Manifest
new file mode 100644
index 000000000..e145fa37f
--- /dev/null
+++ b/sci-libs/matio/Manifest
@@ -0,0 +1,4 @@
+DIST matio-1.3.1.tar.gz 938713 RMD160 64e12e1774db3054ce11f6efd15686c8432a3197 SHA1 70af161a788f7f5e171f27e2655763454ec33839 SHA256 5c8e5df8500c4e444865f65e94ba2b1084a0a370733195655099f5c6f2069eb0
+EBUILD matio-1.3.1.ebuild 914 RMD160 eb29d7b49384781c1a9f5d597613df2f80cb5885 SHA1 62d8c149d89d04a83a4765ff0763a2dcb5673996 SHA256 73931df6056b3a856b16b174342ce7e536aee0ca95ee465a4ec1db38f6186e04
+MISC ChangeLog 614 RMD160 4f8e87a9ab63a5a191d44506e709bb6b12b4053f SHA1 02008a45278e5c147425e2878c2edb14bb4c6b1a SHA256 b484aadb1ab72c5b263ba70a319a48e95afaff6f5e580a5c09a5d44abdc00847
+MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900
diff --git a/sci-libs/matio/matio-1.3.1.ebuild b/sci-libs/matio/matio-1.3.1.ebuild
new file mode 100644
index 000000000..a5cc1da74
--- /dev/null
+++ b/sci-libs/matio/matio-1.3.1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils fortran
+
+DESCRIPTION="Library for reading and writing matlab .mat files"
+HOMEPAGE="http://sourceforge.net/projects/matio/"
+SLOT="0"
+LICENSE="LGPL-2"
+KEYWORDS="~x86 ~amd64"
+IUSE="doc fortran"
+SRC_URI="mirror://sourceforge/matio/${P}.tar.gz"
+DEPEND="doc? ( app-doc/doxygen virtual/tetex )"
+FORTRAN="gfortran"
+
+#### Remove the following line when moving this ebuild to the main tree!
+RESTRICT="nomirror"
+
+pkg_setup() {
+ use fortran && fortran_pkg_setup
+}
+
+src_compile() {
+ addwrite /var/cache/fonts
+ addwrite /usr/share/texmf
+ econf --enable-shared \
+ --disable-test \
+ $(use_enable fortran ) \
+ $(use_enable doc docs ) \
+ || die "econf failed"
+ emake || die "emake failed"
+}
+
+src_install() {
+ make DESTDIR="${D}" install || die "make install failed"
+ dodoc README ChangeLog
+}
diff --git a/sci-libs/matio/metadata.xml b/sci-libs/matio/metadata.xml
new file mode 100644
index 000000000..b229aec85
--- /dev/null
+++ b/sci-libs/matio/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-libs/mkl/Manifest b/sci-libs/mkl/Manifest
new file mode 100644
index 000000000..3e2c49474
--- /dev/null
+++ b/sci-libs/mkl/Manifest
@@ -0,0 +1,4 @@
+AUX mkl-10.0.2.018-openmpi.patch 332 RMD160 255a2cb3fdba6fd1803d830e9cd791da954d958f SHA1 6a3a7b690873c9bc4c003f47739dfa9394ab9627 SHA256 758c3aef0124932426002aa502c0e7b721a026d6c54c37c679d3ee7eb607b58c
+AUX mkl-10.0.2.018-tests.patch 528 RMD160 15f11a38567bd533626008fce62e6021372bfc53 SHA1 8c9358d798f597e87d8a62fff27b79123273ebe3 SHA256 f65a074c64a3969b08d41f88874f25fdc06693b5a5aee930bd7ef9763e94e71d
+DIST l_mkl_p_10.0.2.018.tgz 227440983 RMD160 0c28416597ef917328193fa0c6403d7c0e7b971d SHA1 1aa8c47701b142ab52ebcda27fdda4c5d0903471 SHA256 311d2885a33d553a2d1b1370eed1e3e9bccc246f2dcd20e3558ed492443ba20f
+EBUILD mkl-10.0.2.018.ebuild 8933 RMD160 87503b074bd00f371a34f6f2f42451453ae3e107 SHA1 8d11e096325f3ea78cd7e1191864a13f4b42f447 SHA256 802e2c328778cda9216d76672bcdf00273ef137d4b7b9354f7e1de2dc784644b
diff --git a/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch b/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch
new file mode 100644
index 000000000..6f7f9edeb
--- /dev/null
+++ b/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch
@@ -0,0 +1,18 @@
+--- interfaces/fftw2x_cdft/makefile.orig 2008-03-11 23:26:26.287984332 +0000
++++ interfaces/fftw2x_cdft/makefile 2008-03-13 10:56:44.755095617 +0000
+@@ -172,6 +172,15 @@
+ endif
+
+
++ifeq ($(mpi),openmpi)
++CS = mpicc
++ifdef mpidir
++_CS = $(mpidir)/bin/$(CS)
++else
++_CS = $(CS)
++endif
++endif
++
+ vpath %.c wrappers
+
+ $(WRP): %.o: %.c
diff --git a/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch b/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch
new file mode 100644
index 000000000..975170f7d
--- /dev/null
+++ b/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch
@@ -0,0 +1,21 @@
+--- tests/scalapack/make.inc.orig 2008-03-13 22:36:06.119890888 +0000
++++ tests/scalapack/make.inc 2008-03-13 22:54:58.201781899 +0000
+@@ -59,6 +59,9 @@
+ IFACE_PART = _ilp64
+ COPTS = -DMKL_ILP64
+ FOPTS = -i8
++ifeq ($(compiler),gnu)
++FOPTS = -fdefault-integer-8
++endif
+ else
+ ADD_IFACE = _lp64
+ IFACE_PART = _lp64
+@@ -203,7 +206,7 @@
+ # Compiler flags
+ F77FLAGS=-w -u $(OPTS)
+ ifeq ($(comp),gnu)
+-F77FLAGS=$(OPTS) -ff90 -fno-globals -Wno-globals
++F77FLAGS=$(OPTS)
+ endif
+ # Remove objects variable
+ RMOBJ=rm -f *.o core work.pc*
diff --git a/sci-libs/mkl/mkl-10.0.2.018.ebuild b/sci-libs/mkl/mkl-10.0.2.018.ebuild
new file mode 100644
index 000000000..e502100ea
--- /dev/null
+++ b/sci-libs/mkl/mkl-10.0.2.018.ebuild
@@ -0,0 +1,327 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils toolchain-funcs fortran check-reqs
+
+PID=967
+PB=${PN}
+DESCRIPTION="Intel(R) Math Kernel Library: linear algebra, fft, math functions"
+HOMEPAGE="http://developer.intel.com/software/products/mkl/"
+
+KEYWORDS="~amd64 ~ia64 ~x86"
+SRC_URI="http://registrationcenter-download.intel.com/irc_nas/${PID}/l_${PN}_p_${PV}.tgz"
+
+#slotting not yet supported (would need a mkl-config)
+#MAJOR=$(get_major_version ${PV})
+#MINOR=$(get_version_component_range 2 ${PV})
+#SLOT="${MAJOR}.${MINOR}"
+
+SLOT="0"
+LICENSE="Intel-SDP"
+
+IUSE="doc fftw fortran95 int64 mpi"
+RESTRICT="strip mirror"
+
+DEPEND="app-admin/eselect-blas
+ app-admin/eselect-cblas
+ app-admin/eselect-lapack"
+
+RDEPEND="${DEPEND}
+ dev-util/pkgconfig
+ doc? ( app-doc/blas-docs app-doc/lapack-docs )
+ mpi? ( virtual/mpi )"
+
+MKL_DIR=/opt/intel/${PN}/${PV}
+
+pkg_setup() {
+
+ # Check the license
+ [[ -z ${MKL_LICENSE} && -d /opt/intel/licenses ]] && \
+ MKL_LICENSE=$(find /opt/intel/licenses -name *MKL*.lic)
+ if [[ -z ${MKL_LICENSE} ]]; then
+ eerror "Did not find any valid mkl license."
+ eerror "Register at ${HOMEPAGE} to receive a license"
+ eerror "and place it in /opt/intel/licenses or run:"
+ eerror "\t MKL_LICENSE=/my/license/dir emerge mkl"
+ die "license setup failed"
+ fi
+
+ # Check if we have enough free diskspace to install
+ CHECKREQS_DISK_BUILD="1100"
+ check_reqs
+
+ # Check and setup fortran
+ FORTRAN="gfortran ifc g77"
+ if use fortran95; then
+ FORTRAN="gfortran ifc"
+ # blas95 and lapack95 don't compile with gfortran < 4.2
+ gcc-version lt 4 2 && FORTRAN="ifc"
+ fi
+ use int64 && FORTRAN="gfortran ifc"
+ fortran_pkg_setup
+ MKL_FC="gnu"
+ [[ ${FORTRANC} == if* ]] && MKL_FC="intel"
+
+ # build profiles according to what compiler is installed
+ MKL_CC="gnu"
+ [[ $(tc-getCC) == icc ]] && MKL_CC="intel"
+
+ if has_version sys-cluster/mpich; then
+ MKL_MPI=mpich
+ elif has_version sys-cluster/mpich2; then
+ MKL_MPI=mpich2
+ elif has_version sys-cluster/openmpi; then
+ MKL_MPI=openmpi
+ elif has_version sys-cluster/lam-mpi; then
+ MKL_MPI=lam-mpi
+ else
+ MKL_MPI=intelmpi
+ fi
+}
+
+src_unpack() {
+
+ unpack ${A}
+ cd l_${PN}_*_${PV}/install
+
+ cp ${MKL_LICENSE} "${WORKDIR}"/
+ MKL_LIC="$(basename ${MKL_LICENSE})"
+
+ # binary blob extractor installs rpm leftovers in /opt/intel
+ addwrite /opt/intel
+ # undocumented features: INSTALLMODE_mkl=NONRPM
+
+ # We need to install mkl non-interactively.
+ # If things change between versions, first do it interactively:
+ # tar xf l_*; ./install.sh --duplicate mkl.ini;
+ # The file will be instman/mkl.ini
+ # Then check it and modify the ebuild-created one below
+ # --norpm is required to be able to install 10.x
+ cat > mkl.ini <<-EOF
+ [MKL]
+ EULA_ACCEPT_REJECT=ACCEPT
+ FLEXLM_LICENSE_LOCATION=${WORKDIR}/${MKL_LIC}
+ INSTALLMODE_mkl=NONRPM
+ INSTALL_DESTINATION=${S}
+ EOF
+ einfo "Extracting ..."
+ ./install \
+ --silent ./mkl.ini \
+ --installpath "${S}" \
+ --log log.txt &> /dev/null
+
+ if [[ -z $(find "${S}" -name libmkl.so) ]]; then
+ eerror "Could not find extracted files"
+ eerror "See ${PWD}/log.txt to see why"
+ die "extracting failed"
+ fi
+
+ # remove unused stuff and set up intel names
+ rm -rf "${WORKDIR}"/l_*
+
+ cd "${S}"
+ # allow openmpi to work
+ epatch "${FILESDIR}"/${P}-openmpi.patch
+ # make scalapack tests work for gfortran
+ epatch "${FILESDIR}"/${P}-tests.patch
+ case ${ARCH} in
+ x86) MKL_ARCH=32
+ MKL_KERN=ia32
+ rm -rf lib*/{em64t,64}
+ ;;
+
+ amd64) MKL_ARCH=em64t
+ MKL_KERN=em64t
+ rm -rf lib*/{32,64}
+ ;;
+
+ ia64) MKL_ARCH=64
+ MKL_KERN=ipf
+ rm -rf lib*/{32,em64t}
+ ;;
+ esac
+ MKL_LIBDIR=${MKL_DIR}/lib/${MKL_ARCH}
+}
+
+src_compile() {
+ cd "${S}"/interfaces
+ if use fortran95; then
+ einfo "Compiling fortan95 static lib wrappers"
+ local myconf="lib${MKL_ARCH}"
+ [[ ${FORTRANC} == gfortran ]] && \
+ myconf="${myconf} FC=gfortran"
+ if use int64; then
+ myconf="${myconf} interface=ilp64"
+ [[ ${FORTRANC} == gfortran ]] && \
+ myconf="${myconf} FOPTS=-fdefault-integer-8"
+ fi
+ for x in blas95 lapack95; do
+ pushd ${x}
+ emake ${myconf} || die "emake ${x} failed"
+ popd
+ done
+ fi
+
+ if use fftw; then
+ local fftwdirs="fftw2xc fftw2xf fftw3xc fftw3xf"
+ local myconf="lib${MKL_ARCH} compiler=${MKL_CC}"
+ if use mpi; then
+ fftwdirs="${fftwdirs} fftw2x_cdft"
+ myconf="${myconf} mpi=${MKL_MPI}"
+ fi
+ einfo "Compiling fftw static lib wrappers"
+ for x in ${fftwdirs}; do
+ pushd ${x}
+ emake ${myconf} || die "emake ${x} failed"
+ popd
+ done
+ fi
+}
+
+src_test() {
+ cd "${S}"/tests
+ local myconf
+ local testdirs="blas cblas"
+ use int64 && myconf="${myconf} interface=ilp64"
+ if use mpi; then
+ testdirs="${testdirs} scalapack"
+ myconf="${myconf} mpi=${MKL_MPI}"
+ fi
+ for x in ${testdirs}; do
+ pushd ${x}
+ einfo "Testing ${x}"
+ emake \
+ compiler=${MKL_FC} \
+ ${myconf} \
+ so${MKL_ARCH} \
+ || die "emake ${x} failed"
+ popd
+ done
+}
+
+mkl_make_generic_profile() {
+ cd "${S}"
+ # produce eselect files
+ # don't make them in FILESDIR, it changes every major version
+ cat > eselect.blas <<-EOF
+ ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libblas.a
+ ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so
+ ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so.0
+ EOF
+ cat > eselect.cblas <<-EOF
+ ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libcblas.a
+ ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so
+ ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so.0
+ ${MKL_DIR}/include/mkl_cblas.h /usr/include/cblas.h
+ EOF
+ cat > eselect.lapack <<-EOF
+ ${MKL_LIBDIR}/libmkl_lapack.a /usr/@LIBDIR@/liblapack.a
+ ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so
+ ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so.0
+ EOF
+}
+
+# usage: mkl_add_profile <profile> <interface_lib> <thread_lib> <rtl_lib>
+mkl_add_profile() {
+ cd "${S}"
+ local prof=${1}
+ insinto ${MKL_LIBDIR}
+ for x in blas cblas lapack; do
+ cat > ${x}-${prof}.pc <<-EOF
+ prefix=/usr
+ libdir=${MKL_LIBDIR}
+ includedir=${prefix}/include
+ Name: ${x}
+ Description: Intel(R) Math Kernel Library implementation of ${p}
+ Version: ${PV}
+ URL: ${HOMEPAGE}
+ Libs: -L\${libdir} ${2} ${3} -lmkl_core ${4} -lpthread
+ EOF
+ cp eselect.${x} eselect.${x}.${prof}
+ echo "${MKL_LIBDIR}/${x}-${prof}.pc /usr/@LIBDIR@/pkgconfig/${x}.pc" \
+ >> eselect.${x}.${prof}
+ doins ${x}-${prof}.pc
+ eselect ${x} add $(get_libdir) eselect.${x}.${prof} ${prof}
+ done
+}
+
+mkl_make_profiles() {
+ local clib
+ has_version 'dev-lang/ifc' && clib="intel"
+ built_with_use sys-devel/gcc fortran && clib="${clib} gf"
+ local slib="-lmkl_sequential"
+ local rlib="-liomp5"
+ for c in ${clib}; do
+ local ilib="-lmkl_${c}_lp64"
+ use x86 && ilib="-lmkl_${c}"
+ local tlib="-lmkl_${c/gf/gnu}_thread"
+ local comp="${c/gf/gfortran}"
+ comp="${comp/intel/ifort}"
+ mkl_add_profile mkl-${comp} ${ilib} ${slib}
+ mkl_add_profile mkl-${comp}-threads ${ilib} ${tlib} ${rlib}
+ if use int64; then
+ ilib="-lmkl_${c}_ilp64"
+ mkl_add_profile mkl-${comp}-int64 ${ilib} ${slib}
+ mkl_add_profile mkl-${comp}-threads-int64 ${ilib} ${tlib} ${rlib}
+ fi
+ done
+}
+
+src_install() {
+ dodir ${MKL_DIR}
+ # upstream installs a link, no idea why
+ dosym ${MKL_DIR} ${MKL_DIR/mkl/cmkl}
+
+ # install license
+ if [[ ! -f /opt/intel/licenses/${MKL_LIC} ]]; then
+ insinto /opt/intel/licenses
+ doins "${WORKDIR}"/${MKL_LIC} || die "install license failed"
+ fi
+
+ # install main stuff: cp faster than doins
+ einfo "Installing files..."
+ local cpdirs="benchmarks doc examples include interfaces lib man tests"
+ local doinsdirs="tools"
+ cp -pPR ${cpdirs} "${D}"${MKL_DIR} \
+ || die "installing mkl failed"
+ doins ${doinsdirs} || die "doins ${doinsdirs} failed"
+
+ # install blas/lapack profiles
+ mkl_make_generic_profile
+ mkl_make_profiles
+
+ # install env variables
+ local env_file=35mkl
+ echo "LDPATH=${MKL_LIBDIR}" > ${env_file}
+ echo "MANPATH=${MKL_DIR}/man" >> ${env_file}
+ doenvd ${env_file} || die "doenvd failed"
+}
+
+pkg_postinst() {
+ # if blas profile is mkl, set lapack and cblas profiles as mkl
+ local blas_lib=$(eselect blas show | cut -d' ' -f2)
+ local def_prof="mkl-gfortran-threads"
+ has_version 'dev-lang/ifc' && def_prof="mkl-ifort-threads"
+ use int64 && def_prof="${def_prof}-int64"
+ for x in blas cblas lapack; do
+ local current_lib=$(eselect ${x} show | cut -d' ' -f2)
+ if [[ -z ${current_lib} || \
+ ${current_lib} == mkl* || \
+ ${blas_lib} == mkl* ]]; then
+ # work around eselect bug #189942
+ local configfile="${ROOT}"/etc/env.d/${x}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${x} set ${def_prof}
+ elog "${x} has been eselected to ${def_prof}"
+ if [[ ${current_lib} != ${blas_lib} ]]; then
+ eselect blas set ${def_prof}
+ elog "${x} is now set to ${def_prof} for consistency"
+ fi
+ else
+ elog "Current eselected ${x} is ${current_lib}"
+ elog "To use one of mkl profiles, issue (as root):"
+ elog "\t eselect ${x} set <profile>"
+ fi
+ done
+}
diff --git a/sci-libs/parmetis/Manifest b/sci-libs/parmetis/Manifest
new file mode 100644
index 000000000..4c01e9be3
--- /dev/null
+++ b/sci-libs/parmetis/Manifest
@@ -0,0 +1,4 @@
+AUX parmetis-3.1-autotools.patch 9832 RMD160 e22e2368f77c827be27cb96680b253879938674c SHA1 f604cfa7d45bb3f97e7afc1ce8b7836035513e2f SHA256 2e2975d80cffefe4dcdbf6632b8bb9d2e0dd789f5404f8dd0965ba41a5b5ca43
+DIST ParMetis-3.1.tar.gz 5286085 RMD160 08996ac3724c18b66ff7fc03c1ffecae4d9206e1 SHA1 831ef886269b7c56412a9cc62116873e796c4b76 SHA256 11485828fe25436dc6d41cb048bc4b744969b51d4b751996007612aa95d5ff16
+EBUILD parmetis-3.1-r1.ebuild 754 RMD160 259f62f1c04614e74e293d9c0cfddddcc304e455 SHA1 40ff7c72a7baaa2cf37e9d0d2299fd2d68059fcf SHA256 f971a40c1cf82e3da7095f7a532ef31977c3f4d50b7320a8d802d4ca0c87d84e
+MISC metadata.xml 567 RMD160 0565f147e7f67469216f64490469c39a78040073 SHA1 619ff63c86b9da320ad0d6af86c83a78e748ef7d SHA256 e7b13d4ac35de3236571c5efd0cbf9143333a4978e9dbe277b45ba3a5b4bd29a
diff --git a/sci-libs/parmetis/files/parmetis-3.1-autotools.patch b/sci-libs/parmetis/files/parmetis-3.1-autotools.patch
new file mode 100644
index 000000000..50455c50d
--- /dev/null
+++ b/sci-libs/parmetis/files/parmetis-3.1-autotools.patch
@@ -0,0 +1,270 @@
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2008-02-05 19:26:56.002301741 +0000
+@@ -0,0 +1,15 @@
++# -*- Autoconf -*-
++AC_PREREQ(2.59)
++AC_INIT(parmetis, 3.1, karypis@cs.umn.edu)
++AM_INIT_AUTOMAKE([foreign])
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++AC_CHECK_LIB(m, sqrt)
++sinclude(acx_mpi.m4)
++AC_LANG_PUSH([C])
++ACX_MPI([], AC_MSG_ERROR([could not compile an mpi test program]))
++AC_CONFIG_FILES([Makefile
++ METISLib/Makefile
++ ParMETISLib/Makefile
++ Programs/Makefile])
++AC_OUTPUT
+--- acx_mpi.m4 1970-01-01 01:00:00.000000000 +0100
++++ acx_mpi.m4 2008-02-01 16:24:54.723228974 +0000
+@@ -0,0 +1,183 @@
++##### http://autoconf-archive.cryp.to/acx_mpi.html
++#
++# SYNOPSIS
++#
++# ACX_MPI([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
++#
++# DESCRIPTION
++#
++# This macro tries to find out how to compile programs that use MPI
++# (Message Passing Interface), a standard API for parallel process
++# communication (see http://www-unix.mcs.anl.gov/mpi/)
++#
++# On success, i