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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
---|---|---|
committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology')
801 files changed, 30735 insertions, 0 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild new file mode 100644 index 000000000000..c76b28f8893a --- /dev/null +++ b/sci-biology/ApE/ApE-2.0.7-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A Plasmid Editor" +HOMEPAGE="http://www.biology.utah.edu/jorgensen/wayned/ape/" +SRC_URI="http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip" + +LICENSE="ApE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="app-arch/unzip" +RDEPEND=" + dev-lang/tcl:0 + dev-lang/tk:0" + +RESTRICT="mirror" + +S="${WORKDIR}/ApE Linux/" + +src_compile() { :; } + +src_install() { + cat >> "${T}/ApE" <<- "EOF" + #!/bin/bash + cmdArgs="" + + # AppMain.tcl searches files relative to the directory where it resides. + # Add absolute path to file here, if necessary. + for rfpath in "$@"; do + afpath="$PWD/${rfpath}" + if test -r "${afpath}"; then + cmdArgs="${cmdArgs} \"${afpath}\""; + else + cmdArgs="${cmdArgs} \"${rfpath}\""; + fi + done + + eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}" + EOF + + dobin "${T}/ApE" + insinto "/usr/share/${P}" + doins -r "${WORKDIR}"/ApE\ Linux/* + make_desktop_entry ${PN} ${PN} \ + "/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \ + "Science" +} diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest new file mode 100644 index 000000000000..c8bc584062a7 --- /dev/null +++ b/sci-biology/ApE/Manifest @@ -0,0 +1 @@ +DIST ApE-2.0.7.zip 318454 SHA256 9d718562ef250b68dfad1de7d4179540fc04c001b0fdc5e9bd70f3605561bc32 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254 WHIRLPOOL d13e8a997c36f8e7ac951a17c195a714a243292f9a99f524758b09b1fdc9f436b11cf1124ac1a3527ff70aa8cc6dc9ac516a910246f9f6e4f8376c78e8b44013 diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml new file mode 100644 index 000000000000..4252fbfae02e --- /dev/null +++ b/sci-biology/ApE/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> + </longdescription> +</pkgmetadata> diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild new file mode 100644 index 000000000000..a3c0228b819d --- /dev/null +++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MODULE_AUTHOR=LDS +inherit perl-module webapp + +DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser" +HOMEPAGE="http://gmod.org/wiki/GBrowse" +KEYWORDS="~amd64 ~x86" +IUSE="-minimal mysql postgres +sqlite" + +SLOT="0" +WEBAPP_MANUAL_SLOT="yes" + +CDEPEND="!<sci-biology/GBrowse-2.44-r1 + >=sci-biology/bioperl-1.6.9 + >=dev-perl/Bio-Graphics-2.09 + >=dev-perl/GD-2.07 + >=dev-perl/CGI-Session-4.02 + dev-perl/IO-String + dev-perl/JSON + dev-perl/libwww-perl + dev-perl/Statistics-Descriptive + !minimal? ( + dev-perl/Bio-Das + >=dev-perl/Bio-SamTools-1.20 + dev-perl/Crypt-SSLeay + dev-perl/DB_File-Lock + dev-perl/DBI + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sqlite? ( dev-perl/DBD-SQLite ) + dev-perl/FCGI + dev-perl/File-NFSLock + dev-perl/GD-SVG + dev-perl/Net-OpenID-Consumer + dev-perl/Net-SMTP-SSL + )" +# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile +DEPEND="dev-perl/Module-Build + dev-perl/Capture-Tiny + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch ) + +src_configure() { + webapp_src_preinst + +# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse" + myconf="--conf=/etc/gbrowse2" + myconf="${myconf} --htdocs=${MY_HTDOCSDIR}" + myconf="${myconf} --cgibin=${MY_CGIBINDIR}" + myconf="${myconf} --tmp=/var/tmp/gbrowse2" + myconf="${myconf} --persistent=/var/db/gbrowse2" + myconf="${myconf} --databases=/var/db/gbrowse2/databases" + myconf="${myconf} --installconf=no" + myconf="${myconf} --installetc=no" + perl-module_src_configure +} + +src_install() { + dodir /var/tmp/gbrowse2 + dodir /var/db/gbrowse2/sessions + dodir /var/db/gbrowse2/userdata + webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2 + perl-module_src_install + webapp_src_install +} diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest new file mode 100644 index 000000000000..204fe59d5aa7 --- /dev/null +++ b/sci-biology/GBrowse/Manifest @@ -0,0 +1 @@ +DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135 diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch new file mode 100644 index 000000000000..5aa0be9df918 --- /dev/null +++ b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch @@ -0,0 +1,72 @@ +diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm +--- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000 ++++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000 +@@ -454,33 +454,33 @@ + $gid =~ /^(\d+)$/; + $gid = $1; + +- unless (chown $uid,$gid,$tmp) { +- $self->ownership_warning($tmp,$user); +- } ++# unless (chown $uid,$gid,$tmp) { ++# $self->ownership_warning($tmp,$user); ++# } + + my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); + my $images = File::Spec->catfile($tmp,'images'); + my $htdocs = $self->install_path->{htdocs}; +- chown $uid,-1,$htdocs; ++# chown $uid,-1,$htdocs; + { + local $> = $uid; +- symlink($images,$htdocs_i); # so symlinkifowner match works! ++# symlink($images,$htdocs_i); # so symlinkifowner match works! + } +- chown $>,-1,$self->install_path->{htdocs}; ++# chown $>,-1,$self->install_path->{htdocs}; + + my $persistent = $self->install_path->{'persistent'}; + my $sessions = File::Spec->catfile($persistent,'sessions'); + my $userdata = File::Spec->catfile($persistent,'userdata'); +- mkpath([$sessions,$userdata],0711); ++# mkpath([$sessions,$userdata],0711); + + my $databases = $self->install_path->{'databases'}; + +- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { +- $self->ownership_warning($databases,$user); +- } ++# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { ++# $self->ownership_warning($databases,$user); ++# } + +- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); +- $self->fix_selinux; ++ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); ++ # $self->fix_selinux; + + my $base = basename($self->install_path->{htdocs}); + +@@ -489,14 +489,14 @@ + my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); + my $perl = $self->perl; + my @inc = map{"-I$_"} split ':',$self->added_to_INC; +- system $perl,@inc,$metadb_script; +- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; ++# system $perl,@inc,$metadb_script; ++# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; + +- if (Module::Build->y_n( +- "It is recommended that you restart Apache. Shall I try this for you?",'y' +- )) { +- system "sudo /etc/init.d/apache2 restart"; +- } ++# if (Module::Build->y_n( ++# "It is recommended that you restart Apache. Shall I try this for you?",'y' ++# )) { ++# system "sudo /etc/init.d/apache2 restart"; ++# } + + print STDERR "\n***INSTALLATION COMPLETE***\n"; + print STDERR "Load http://localhost/$base for demo and documentation.\n"; +Only in GBrowse-2.39/install_util: GBrowseInstall.pm~ diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml new file mode 100644 index 000000000000..32b15c723f9d --- /dev/null +++ b/sci-biology/GBrowse/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-biology</herd> +<upstream> + <remote-id type="cpan">GBrowse</remote-id> +</upstream> +</pkgmetadata> diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest new file mode 100644 index 000000000000..7b3eeafe5263 --- /dev/null +++ b/sci-biology/aaindex/Manifest @@ -0,0 +1 @@ +DIST aaindex-9.1.tar.bz2 133780 RMD160 6f5bd699de3c84bd366f9747f57712ba8aecf513 SHA1 7215e3dae85cd61919854ba5dd5abff29be91852 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa diff --git a/sci-biology/aaindex/aaindex-9.1.ebuild b/sci-biology/aaindex/aaindex-9.1.ebuild new file mode 100644 index 000000000000..6c45282be145 --- /dev/null +++ b/sci-biology/aaindex/aaindex-9.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Amino acid indices and similarity matrices" +LICENSE="public-domain" +HOMEPAGE="http://www.genome.ad.jp/aaindex" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" + +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir AAINDEX + echo + einfo "Indexing AAindex for usage with EMBOSS." + EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die \ + "Indexing AAindex failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins ${PN}{1,2,3} || die "Failed to install raw database." + fi + dodoc ${PN}.doc || die "Failed to install documentation." + if use emboss; then + insinto /usr/share/EMBOSS/data/AAINDEX + doins AAINDEX/* || die "Failed to install EMBOSS data files." + fi +} diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml new file mode 100644 index 000000000000..ccb567e64e02 --- /dev/null +++ b/sci-biology/aaindex/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + Amino acid indices and similarity matrices maintained at Kyoto + University. An amino acid index is a set of 20 numerical values + representing any of the different physicochemical and biological + properties of amino acids. The AAindex1 section of the Amino Acid + Index Database is a collection of published indices together with the + result of cluster analysis using the correlation coefficient as the + distance between two indices. This section currently contains 494 + indices. Another important feature of amino acids that can be + represented numerically is the similarity between amino acids. Thus, a + similarity matrix, also called a mutation matrix, is a set of 210 + numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used + for sequence alignments and similarity searches. The AAindex2 section + of the Amino Acid Index Database is a collection of published amino + acid mutation matrices together with the result of cluster analysis. + This section currently contains 83 matrices. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest new file mode 100644 index 000000000000..77dfde1ec9c8 --- /dev/null +++ b/sci-biology/abyss/Manifest @@ -0,0 +1,3 @@ +DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914 +DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01 +DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07 diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild new file mode 100644 index 000000000000..08a82e2f692a --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="amd64 x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +src_prepare() { + tc-export AR + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-ac_prog_ar.patch + + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + econf \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable openmp) +} diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild new file mode 100644 index 000000000000..e230da8847ff --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.4.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild new file mode 100644 index 000000000000..04dcc7ce6a25 --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.6.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + dev-libs/boost + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-ac_prog_ar.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch new file mode 100644 index 000000000000..300868f52b76 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 5c6cb92..b99bedd 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + + # Checks for header files. + AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch new file mode 100644 index 000000000000..42066f7f2152 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 506ea0c..a0a403c 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -15,6 +15,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch new file mode 100644 index 000000000000..c2cc35c31d98 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch new file mode 100644 index 000000000000..158e9b1262e4 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 9d4bb66..aa94364 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) + diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch new file mode 100644 index 000000000000..c2cc35c31d98 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/abyss/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/allpathslg/Manifest b/sci-biology/allpathslg/Manifest new file mode 100644 index 000000000000..8209935b6d9e --- /dev/null +++ b/sci-biology/allpathslg/Manifest @@ -0,0 +1,3 @@ +DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9 +DIST allpathslg-47093.tar.gz 3057279 SHA256 493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512 499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314 WHIRLPOOL a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc +DIST allpathslg-52415.tar.gz 3129266 SHA256 3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512 afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6 WHIRLPOOL de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785 diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild b/sci-biology/allpathslg/allpathslg-42337.ebuild new file mode 100644 index 000000000000..9fb44dfcc905 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-42337.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + sed -i 's/-ggdb3//' configure.ac || die + eautoreconf +} + +src_install() { + einstall || die + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${D}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild b/sci-biology/allpathslg/allpathslg-47093.ebuild new file mode 100644 index 000000000000..ab971ec46c89 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-47093.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools eutils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc4.9.patch + sed -i 's/-ggdb//' configure.ac || die + eautoreconf +} + +src_install() { + default + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${ED}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild new file mode 100644 index 000000000000..29de20e37670 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-52415.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="openmp" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +pkg_pretend() { + # as of release 44849, GCC 4.7.0 (or higher) is required + # seems pre gcc-4.7 users must stay with: + # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz + if [[ ${MERGE_TYPE} != binary ]]; then + [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \ + die "You need to use gcc >4.7" + fi +} + +src_prepare() { + local i + sed \ + -e 's/-ggdb//' \ + -e 's:CEHCK:CHECK:g' \ + -i configure.ac || die + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + sed -e "/bin_PROGRAMS/s: ${i} : :g" -i src/Makefile.am || die + done + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch new file mode 100644 index 000000000000..46e5493d28ce --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch @@ -0,0 +1,16 @@ + src/paths/long/VariantCallTools.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/paths/long/VariantCallTools.cc b/src/paths/long/VariantCallTools.cc +index dfe2787..725878b 100644 +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1674,7 +1674,7 @@ void EdgesOnRef::FindAllPathsNoLoop(const GraphT& dg, int entrace_edge, int exit + int n1 = to_right2[entrace_edge]; + int n2 = to_left2[exit_edge]; + +- PartialPath start = {{n1},{}}; ++ PartialPath start{{n1},vec<int>{}}; + stack<PartialPath> visited; + visited.push(start); + while (! visited.empty()) { diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/allpathslg/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/amap/Manifest b/sci-biology/amap/Manifest new file mode 100644 index 000000000000..35e082de93b9 --- /dev/null +++ b/sci-biology/amap/Manifest @@ -0,0 +1 @@ +DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4 diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild new file mode 100644 index 000000000000..389102a8e757 --- /dev/null +++ b/sci-biology/amap/amap-2.2-r2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2 + +MY_P=${PN}.${PV} + +DESCRIPTION="Protein multiple-alignment-based sequence annealing" +HOMEPAGE="http://bio.math.berkeley.edu/amap/" +SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="java" + +RDEPEND="java? ( >=virtual/jre-1.5 )" +DEPEND="java? ( >=virtual/jdk-1.5 )" + +S=${WORKDIR}/${PN}-align + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-includes.patch +} + +src_compile() { + emake -C align CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed" + + if use java; then + pushd "${S}"/display + eant -Ddisplay all || die + popd + fi +} + +src_install() { + dobin align/${PN} || die + dodoc align/{README,PROBCONS.README} || die + insinto /usr/share/${PN}/examples + doins examples/* || die + if use java; then + java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar + java-pkg_dolauncher amapdisplay --jar amapdisplay.jar + fi +} diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch new file mode 100644 index 000000000000..77c4261db5cf --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-includes.patch @@ -0,0 +1,44 @@ +Fixes build with gcc 4.3 and 4.6 + +http://bugs.gentoo.org/217921 +http://bugs.gentoo.org/360517 + +--- amap-align/align/Amap.cc ++++ amap-align/align/Amap.cc +@@ -12,6 +12,8 @@ + #include "ProbabilisticModel.h" + #include "EvolutionaryTree.h" + #include "SparseMatrix.h" ++#include <limits> ++#include <climits> + #include <string> + #include <sstream> + #include <iomanip> +@@ -23,6 +25,7 @@ + #include <cstdlib> + #include <cerrno> + #include <iomanip> ++#include <cstring> + + string parametersInputFilename = ""; + string parametersOutputFilename = "no training"; +--- amap-align/align/MultiSequenceDag.h ++++ amap-align/align/MultiSequenceDag.h +@@ -13,6 +13,7 @@ + #include <map> + #include <queue> + #include <iostream> ++#include <limits> + #include "MultiSequence.h" + #include "SparseMatrix.h" + +--- amap-align/align/SafeVector.h.org 2011-03-26 11:50:11.935069583 +0100 ++++ amap-align/align/SafeVector.h 2011-03-26 11:50:21.112553151 +0100 +@@ -9,6 +9,7 @@ + #define SAFEVECTOR_H + + #include <cassert> ++#include <cstddef> + #include <vector> + + ///////////////////////////////////////////////////////////////// diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch new file mode 100644 index 000000000000..5a9841c98255 --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -0,0 +1,35 @@ +Respect {CXX,LD}FLAGS + +http://bugs.gentoo.org/332009 + +--- amap-align/align/Makefile ++++ amap-align/align/Makefile +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' + + # debug mode +@@ -26,8 +28,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +- ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + ################################################################################ + # 3) Dependencies + ################################################################################ + +@@ -38,7 +37,7 @@ + all : $(TARGETS) + + amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc +- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm + + .PHONY : clean + clean: diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml new file mode 100644 index 000000000000..34294c65ca04 --- /dev/null +++ b/sci-biology/amap/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/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000000..27ad50ff28ed --- /dev/null +++ b/sci-biology/amos/Manifest @@ -0,0 +1 @@ +DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild new file mode 100644 index 000000000000..a4c860bdbe7f --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="qt4" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch +} + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 +} diff --git a/sci-biology/amos/amos-3.1.0.ebuild b/sci-biology/amos/amos-3.1.0.ebuild new file mode 100644 index 000000000000..945ec9f41b4c --- /dev/null +++ b/sci-biology/amos/amos-3.1.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="qt4" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch +} diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000000..de2a41184c52 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000000..97a8f59d0208 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml new file mode 100644 index 000000000000..a73ee9189a98 --- /dev/null +++ b/sci-biology/amos/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-biology</herd> + <upstream> + <remote-id type="sourceforge">amos</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest new file mode 100644 index 000000000000..7ec0fa4e73a4 --- /dev/null +++ b/sci-biology/arb/Manifest @@ -0,0 +1,7 @@ +DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f +DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43 +DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf +DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984 +DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583 +DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe +DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958 diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild new file mode 100644 index 000000000000..7db2d798ec55 --- /dev/null +++ b/sci-biology/arb/arb-5.1-r1.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + mirror://gentoo/${P}-glibc2.10.patch.bz2 + http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2" + +LICENSE="arb" +SLOT="0" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +RDEPEND="${DEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-glibc2.10.patch\ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/${PV}-libs.patch \ + "${FILESDIR}"/${PV}-bfr-overflow.patch + sed -i \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's/--export-dynamic/-Wl,--export-dynamic/g' \ + "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links || die +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" || die +} diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild new file mode 100644 index 000000000000..97f7dc5dfbdd --- /dev/null +++ b/sci-biology/arb/arb-5.2.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/${PV}-libpng15.patch \ + "${FILESDIR}"/${P}-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's:-O4::g' \ + -e 's:-pipe::g' \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild new file mode 100644 index 000000000000..97f8b78ddca2 --- /dev/null +++ b/sci-biology/arb/arb-5.3.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/5.2-libpng15.patch \ + "${FILESDIR}"/${PN}-5.2-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch new file mode 100644 index 000000000000..21d21f5ac17f --- /dev/null +++ b/sci-biology/arb/files/5.1-bfr-overflow.patch @@ -0,0 +1,16 @@ + ARB_GDE/GDE_HGLfile.cxx | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx +index e353a89..f69635a 100644 +--- a/ARB_GDE/GDE_HGLfile.cxx ++++ b/ARB_GDE/GDE_HGLfile.cxx +@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type) + if(this_elem->id[0] == '\0') + strncpy(this_elem->id,uniqueID(),79); + if(this_elem->short_name[0] == '\0') +- strncpy(this_elem->short_name,this_elem->id,79); ++ strncpy(this_elem->short_name,this_elem->id,31); + if(this_elem->seqlen == 0) + this_elem->protect= + PROT_BASE_CHANGES+ diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch new file mode 100644 index 000000000000..bf0bacad3286 --- /dev/null +++ b/sci-biology/arb/files/5.1-libs.patch @@ -0,0 +1,16 @@ +diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl +index b653a66..b346c96 100644 +--- a/SOURCE_TOOLS/provide_libs.pl ++++ b/SOURCE_TOOLS/provide_libs.pl +@@ -118,11 +118,6 @@ sub provide_libs($$$) { + foreach my $lib (keys %needed_by) { + update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir); + } +- if ($opengl==1) { +- foreach my $lib (keys %needed_by_opengl) { +- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir); +- } +- } + } + + sub main() { diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch new file mode 100644 index 000000000000..3d750e76efe3 --- /dev/null +++ b/sci-biology/arb/files/5.2-libpng15.patch @@ -0,0 +1,45 @@ +Fix building with libpng-1.5 + +https://bugs.gentoo.org/show_bug.cgi?id=378353 + +Patch written by Samuli Suominen <ssuominen@gentoo.org> +--- a/GL/glpng/glpng.c ++++ b/GL/glpng/glpng.c +@@ -285,7 +285,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -390,7 +390,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -569,7 +569,7 @@ + #define ALPHA *q + + switch (trans) { +- case PNG_CALLBACK: ++ case PNG_CALLBACKT: + FORSTART + ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b); + FOREND +--- a/GL/glpng/glpng.h ++++ b/GL/glpng/glpng.h +@@ -57,7 +57,7 @@ + #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS + + /* Transparency parameters */ +-#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */ ++#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */ + #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */ + #define PNG_SOLID -1 /* No transparency */ + #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */ diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch new file mode 100644 index 000000000000..186e78e450b3 --- /dev/null +++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch @@ -0,0 +1,15 @@ + AWTI/AWTI_import.cxx | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx +index 8e730ac..e3f9ff4 100644 +--- a/AWTI/AWTI_import.cxx ++++ b/AWTI/AWTI_import.cxx +@@ -12,6 +12,7 @@ + #include <GEN.hxx> + + #include <climits> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/arb/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/ariadne/Manifest b/sci-biology/ariadne/Manifest new file mode 100644 index 000000000000..a4bf86d55d3c --- /dev/null +++ b/sci-biology/ariadne/Manifest @@ -0,0 +1 @@ +DIST ariadne-1.3.tar.Z 69427 SHA256 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289 WHIRLPOOL 460d8acf2bb49e097a9544ecc089ca60c3478b64ab4d903bd6ee801eccd62fc560bdccf1454c9f22632081cbf1df35de09a4f81d6c131d3f52f36753bc692927 diff --git a/sci-biology/ariadne/ariadne-1.3-r1.ebuild b/sci-biology/ariadne/ariadne-1.3-r1.ebuild new file mode 100644 index 000000000000..80a05b612ca9 --- /dev/null +++ b/sci-biology/ariadne/ariadne-1.3-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs eutils + +DESCRIPTION="Protein sequences and profiles comparison" + +HOMEPAGE="http://www.well.ox.ac.uk/ariadne/" +SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z" + +LICENSE="ARIADNE" +SLOT="0" +KEYWORDS="~amd64 x86" +IUSE="" + +DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/SRC-${PV}" + +src_unpack(){ + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-gcc4.patch + sed -e "s/CC = gcc/CC = $(tc-getCC)/" \ + -e "s/OPTIMISE = -O2/OPTIMISE = ${CFLAGS}/" \ + -i Makefile || die + sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die +} + +src_install() { + dobin Linux/{ariadne,prospero} || die + dolib Linux/libseq.a || die + insinto /usr/include/${PN} + doins Include/*.h || die + dodoc README || die +} diff --git a/sci-biology/ariadne/ariadne-1.3-r2.ebuild b/sci-biology/ariadne/ariadne-1.3-r2.ebuild new file mode 100644 index 000000000000..1fa55ce322db --- /dev/null +++ b/sci-biology/ariadne/ariadne-1.3-r2.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Protein sequences and profiles comparison" +HOMEPAGE="http://www.well.ox.ac.uk/ariadne/" +SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z" + +LICENSE="ARIADNE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/SRC-${PV} + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc4.patch \ + "${FILESDIR}"/${P}-implicits.patch + sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045 + sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die +} + +src_compile() { + emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}" +} + +src_install() { + dobin Linux/{ariadne,prospero} + use static-libs && dolib.a Linux/libseq.a + insinto /usr/include/${PN} + doins Include/*.h || die + dodoc README || die +} diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch new file mode 100644 index 000000000000..0192efd4db5e --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch @@ -0,0 +1,10 @@ +--- cl.c.old 2006-09-12 17:13:02.000000000 -0400 ++++ cl.c 2006-09-12 17:13:34.000000000 -0400 +@@ -658,6 +658,7 @@ + fclose(fp); + if ( ! stat( filename, &buf ) ) + { ++ char *ctime(), *t; + sprintf( date, "%s", ctime(&buf.st_mtime) ); + t = date; + while ( *t ) diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch new file mode 100644 index 000000000000..31c442b12265 --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch @@ -0,0 +1,23 @@ +topalign.c:96:5: warning: implicit declaration of function ‘toupper’ +prospero.c:63:3: warning: implicit declaration of function ‘strcpy’ + +--- SRC-1.3/prospero.c ++++ SRC-1.3/prospero.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<string.h> + #include<math.h> + #include"cl.h" + #include"seq_util.h" +--- SRC-1.3/topalign.c ++++ SRC-1.3/topalign.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<ctype.h> + #include<math.h> + #include"seq_util.h" + #include"ariadne.h" diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml new file mode 100644 index 000000000000..3e55c00f9d7b --- /dev/null +++ b/sci-biology/ariadne/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-biology</herd> + <longdescription> + ARIADNE is a package of two programs, ariadne and prospero, that + compare protein sequences and profiles using the Smith-Waterman + algorithm, and assesses statistical significance using a new accurate + formula, described in Mott, 2000, "Accurate Formula for P-values of + gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. + The sequence/profile comparison algorithms used in ARIADNE are + standard, and are probably not the fastest implementations available. + The novel part is the method for determining statistical significance, + which will give thresholds of significance that are accurate to within + 5% 95% of the time. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000000..cdfb577937e0 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1 @@ +DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild new file mode 100644 index 000000000000..e58be6db6d6a --- /dev/null +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="examples" + +S="${WORKDIR}/${PN}.${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch new file mode 100644 index 000000000000..39cd0762b1c1 --- /dev/null +++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch @@ -0,0 +1,156 @@ + Makefile | 8 +++--- + scripts/Makefile | 6 +++- + scripts/aln2wig/Makefile | 8 +++--- + scripts/compileSpliceCands/Makefile | 6 ++-- + src/Makefile | 43 ++++++++++++++++++---------------- + 5 files changed, 38 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index e23a667..64610c8 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,9 +3,9 @@ + # + + all: +- cd src && ${MAKE} +- cd scripts && ${MAKE} ++ $(MAKE) -C src ++ $(MAKE) -C scripts + + clean: +- cd src && ${MAKE} clean +- cd scripts && ${MAKE} clean ++ $(MAKE) -C src clean ++ $(MAKE) -C scripts clean +diff --git a/scripts/Makefile b/scripts/Makefile +index 6d4dd67..ab6a885 100644 +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,5 +1,7 @@ + all : +- cd aln2wig && ${MAKE} ++ $(MAKE) -C aln2wig ++ $(MAKE) -C compileSpliceCands + + clean : +- cd aln2wig && ${MAKE} clean ++ $(MAKE) -C aln2wig clean ++ $(MAKE) -C compileSpliceCands +diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile +index 64d09f5..9752980 100644 +--- a/scripts/aln2wig/Makefile ++++ b/scripts/aln2wig/Makefile +@@ -1,10 +1,10 @@ +-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb ++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic + + psl2wig : aln2wig.o +- gcc $(CFLAGS) -o aln2wig aln2wig.o; +- cp aln2wig ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; ++ cp aln2wig ../../bin/ + psl2wig.o : aln2wig.c +- gcc $(CFLAGS) -c aln2wig.c ++ $(CC) $(CFLAGS) -c aln2wig.c + + all : psl2wig + +diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile +index cddada5..8079791 100644 +--- a/scripts/compileSpliceCands/Makefile ++++ b/scripts/compileSpliceCands/Makefile +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc -o compileSpliceCands compileSpliceCands.o list.o; +-# cp compileSpliceCands ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ cp compileSpliceCands ../../bin/ + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi -c compileSpliceCands.c ++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c + + all : compileSpliceCands + +diff --git a/src/Makefile b/src/Makefile +index 71795b6..732b953 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,8 +6,8 @@ + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. + # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) + # +-CC = g++ +-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static ++CXX ?= g++ ++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static + INCLS = -I../include -I. + LIBS = # -lcwd + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ +@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte + PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign + INFO = cflags + +-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info ++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin + + .SUFFIXES: + .SUFFIXES: .cc .o .so + + .cc.o: +- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) ++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) + +-augustus: augustus.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++bin: $(PROGR) ++ cp $(PROGR) ../bin/ ++ ++augustus: augustus.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp augustus ../bin/ + +-etraining: etraining.cc $(TOBJS) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++etraining: etraining.o $(TOBJS) $(OBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp etraining ../bin/ + +-evaluate: evaluate.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++evaluate: evaluate.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-consensusFinder: consensusFinder.cc consensus.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++consensusFinder: consensusFinder.o consensus.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-curve2hints: curve2hints.cc exon_seg.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++curve2hints: curve2hints.o exon_seg.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ ++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ + types.o properties.o geneticcode.o pp_profile.o lldouble.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp fastBlockSearch ../bin/ + +-prepareAlign: pp_prepare_align.cc +- $(CC) $(CFLAGS) -o $@ $^ ++prepareAlign: pp_prepare_align.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ + cp prepareAlign ../bin/ + + info: +- echo "$(CFLAGS)" > $(INFO) ++ echo "$(CXXFLAGS)" > $(INFO) + + clean: +- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* + + tidy: clean + rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO) diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/augustus/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/bamtools/Manifest b/sci-biology/bamtools/Manifest new file mode 100644 index 000000000000..1c1972c599d5 --- /dev/null +++ b/sci-biology/bamtools/Manifest @@ -0,0 +1,2 @@ +DIST bamtools-1.0.2.tar.gz 207523 SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512 1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244 WHIRLPOOL 9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990 +DIST bamtools-2.3.0.tar.gz 539446 SHA256 288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af SHA512 432f66384cffc04ab6bc7dc66d8f7b79c1e468d0068db4cabb5cac05f9b6bef7968eff71ffb3ee51b84e23d9bb66a11ef267024138f40116c25e7f18e7210a5c WHIRLPOOL dd888f67c3d0b0ce2f5f2875e242e5df0d54cefd13693230b5f10eb57dd780304b601027cf65f6598a54061a7166903bf06c6c9a46939f6ce6bbb246cab89993 diff --git a/sci-biology/bamtools/bamtools-1.0.2.ebuild b/sci-biology/bamtools/bamtools-1.0.2.ebuild new file mode 100644 index 000000000000..08c40d0705d3 --- /dev/null +++ b/sci-biology/bamtools/bamtools-1.0.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" +HOMEPAGE="https://github.com/pezmaster31/bamtools" +SRC_URI="mirror://github/pezmaster31/bamtools/"${P}".tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="sys-libs/zlib" +RDEPEND="${DEPEND}" + +src_install() { + for i in bin/bamtools-${PV} lib/libbamtools.so.${PV} lib/libbamtools-utils.so.${PV}; do + TMPDIR="$(pwd)" scanelf -Xr $i || die + done + + dobin bin/bamtools + dolib lib/* + insinto /usr/include/bamtools/api + doins include/api/* + insinto /usr/include/bamtools/shared + doins include/shared/* + dodoc README +} diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild b/sci-biology/bamtools/bamtools-2.3.0.ebuild new file mode 100644 index 000000000000..cb86750cc0cf --- /dev/null +++ b/sci-biology/bamtools/bamtools-2.3.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" +HOMEPAGE="https://github.com/pezmaster31/bamtools" +SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + >=dev-libs/jsoncpp-0.5.0-r1 + sys-libs/zlib" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-unbundle.patch ) + +src_install() { + cmake-utils_src_install + use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a +} diff --git a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch new file mode 100644 index 000000000000..318396e75c36 --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch @@ -0,0 +1,32 @@ + src/CMakeLists.txt | 1 - + src/api/CMakeLists.txt | 4 ++-- + src/toolkit/bamtools_filter.cpp | 2 +- + 3 files changed, 3 insertions(+), 4 deletions(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index e359695..2bd2185 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -6,7 +6,6 @@ + # ========================== + + add_subdirectory( api ) +-add_subdirectory( third_party ) + add_subdirectory( toolkit ) + add_subdirectory( utils ) + +diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt +index 66eb35f..65f4639 100644 +--- a/src/api/CMakeLists.txt ++++ b/src/api/CMakeLists.txt +@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} ) + target_link_libraries( BamTools-static ${APILibs} ) + + # set library install destinations +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin") ++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}") + + # export API headers + include(../ExportHeader.cmake) diff --git a/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch new file mode 100644 index 000000000000..c07c59d2cddd --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch @@ -0,0 +1,23 @@ +--- bamtools-2.3.0/src/api/CMakeLists.txt.ori 2013-08-27 18:00:43.000000000 +0200 ++++ bamtools-2.3.0/src/api/CMakeLists.txt 2013-08-27 18:00:47.000000000 +0200 +@@ -54,8 +54,8 @@ + target_link_libraries( BamTools-static ${APILibs} ) + + # set library install destinations +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin") ++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}") + + # export API headers + include(../ExportHeader.cmake) +--- bamtools-2.3.0/src/CMakeLists.txt.ori 2013-08-27 18:03:10.000000000 +0200 ++++ bamtools-2.3.0/src/CMakeLists.txt 2013-08-27 18:03:23.000000000 +0200 +@@ -6,7 +6,6 @@ + # ========================== + + add_subdirectory( api ) +-add_subdirectory( third_party ) + add_subdirectory( toolkit ) + add_subdirectory( utils ) + diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml new file mode 100644 index 000000000000..f2c00c1fdd0c --- /dev/null +++ b/sci-biology/bamtools/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> + <herd>proxy-maintainers</herd> + <maintainer> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest new file mode 100644 index 000000000000..7fd843d7d423 --- /dev/null +++ b/sci-biology/beast-mcmc/Manifest @@ -0,0 +1,2 @@ +DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a +DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5 diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild new file mode 100644 index 000000000000..d25ed786a751 --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +#inherit java-pkg-2 java-ant-2 eutils subversion +inherit java-pkg-2 java-ant-2 eutils + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +#SRC_URI="" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS="dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext + java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-1 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples || die + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild new file mode 100644 index 000000000000..35993562814c --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +#inherit java-pkg-2 java-ant-2 eutils subversion +inherit java-pkg-2 java-ant-2 eutils + +MY_P=BEASTv${PV} + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +#SRC_URI="" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS=" + dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die + #rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext +# java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-2 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) +} diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild new file mode 100644 index 000000000000..30c1a3751011 --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +inherit java-pkg-2 java-ant-2 eutils subversion + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +SRC_URI="" +#SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS="dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext + java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-1 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples || die + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/beast-mcmc/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/bedtools/Manifest b/sci-biology/bedtools/Manifest new file mode 100644 index 000000000000..e8ecdb88e2ea --- /dev/null +++ b/sci-biology/bedtools/Manifest @@ -0,0 +1,2 @@ +DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 +DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84 diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild new file mode 100644 index 000000000000..7de4f347c710 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.16.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +HOMEPAGE="http://code.google.com/p/bedtools/" +SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +S="${WORKDIR}/BEDTools-Version-${PV}" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed -i \ + -e '/export CXXFLAGS/ d' \ + -e '/export CXX/ d' \ + Makefile || die +} + +src_install() { + dobin bin/* + dodoc README* RELEASE_HISTORY + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild new file mode 100644 index 000000000000..cdba954f6d27 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.20.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +HOMEPAGE="http://code.google.com/p/bedtools/" +SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +S="${WORKDIR}/bedtools2-${PV}" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed -i \ + -e '/export CXXFLAGS/ d' \ + -e '/export CXX/ d' \ + Makefile || die +} + +src_install() { + dobin bin/* + dodoc README* RELEASE_HISTORY + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml new file mode 100644 index 000000000000..6edffa4a6dc3 --- /dev/null +++ b/sci-biology/bedtools/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-biology</herd> + <herd>proxy-maintainers</herd> + <maintainer> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription> + BEDTools: a flexible suite of utilities for comparing genomic features. + </longdescription> + <upstream> + <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest new file mode 100644 index 000000000000..532e6e077652 --- /dev/null +++ b/sci-biology/bfast/Manifest @@ -0,0 +1 @@ +DIST bfast-0.7.0a.tar.gz 2456617 SHA256 ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 WHIRLPOOL f9098c00a2f328fd5116447aae86f0aed078f6c2e6a49a4459e09f0c2a2023e0d60be1893fc2337b85444c24efb2636953517eda2ced336d1bc6dc8d94706e6b diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild new file mode 100644 index 000000000000..908334354033 --- /dev/null +++ b/sci-biology/bfast/bfast-0.7.0a.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Blat-like Fast Accurate Search Tool" +HOMEPAGE="https://sourceforge.net/projects/bfast/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="test" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="dev-perl/XML-Simple" + +src_prepare() { + sed \ + -e 's/-m64//' \ + -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \ + -e 's:-g -O2::g' \ + -i configure.ac || die + sed \ + -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \ + -i tests/*sh || die + + sed \ + -e '/docdir/d' \ + -i Makefile.am || die + + use test && AUTOTOOLS_IN_SOURCE_BUILD=1 + + autotools-utils_src_prepare +} diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml new file mode 100644 index 000000000000..45107864e217 --- /dev/null +++ b/sci-biology/bfast/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-biology</herd> + <upstream> + <remote-id type="sourceforge">bfast</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest new file mode 100644 index 000000000000..0bd1b4ccfa7a --- /dev/null +++ b/sci-biology/biogrep/Manifest @@ -0,0 +1 @@ +DIST biogrep-1.0.tar.gz 71867 RMD160 8f22aaa432febbf7d433402ca5da1afe7a98a217 SHA1 b4c24777e94d9f04dfda0d2d6a4599e3bc470a4f SHA256 15421d79f6f16d6bf9bef132a97f7f9ede1bd42d3fb90572df04a1e1abd8cfd8 diff --git a/sci-biology/biogrep/biogrep-1.0-r1.ebuild b/sci-biology/biogrep/biogrep-1.0-r1.ebuild new file mode 100644 index 000000000000..f4af74c73bff --- /dev/null +++ b/sci-biology/biogrep/biogrep-1.0-r1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit toolchain-funcs + +DESCRIPTION="Multithreading application for matching large sets of patternsagainst biosequence dbs" +HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml" +SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_prepare() { + tc-export CC +} + +src_install() { + emake prefix="${D}"/usr install || die "install failed" + dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed" +} diff --git a/sci-biology/biogrep/biogrep-1.0.ebuild b/sci-biology/biogrep/biogrep-1.0.ebuild new file mode 100644 index 000000000000..b2161dcaae5b --- /dev/null +++ b/sci-biology/biogrep/biogrep-1.0.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Multithreading application for matching large sets of patterns +against biosequence dbs." +HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml" +SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz" +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_install() { + emake prefix="${D}"/usr install || die "install failed" + dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed" +} diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml new file mode 100644 index 000000000000..173e3b48f53e --- /dev/null +++ b/sci-biology/biogrep/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-biology</herd> +<maintainer> + <email>jlec@gentoo.org</email> +</maintainer> +</pkgmetadata> + diff --git a/sci-biology/biojava/Manifest b/sci-biology/biojava/Manifest new file mode 100644 index 000000000000..3a20f1c431f2 --- /dev/null +++ b/sci-biology/biojava/Manifest @@ -0,0 +1,2 @@ +DIST biojava-1.6-all.jar 24571007 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e SHA512 300bd6e02fe052c810c52cb2cc4255628bee704af187ad746b97e57941778dc3a1996b3917db021d74db8c716f94c90c94c5a5e2d4bc212c06259381045f3034 WHIRLPOOL e5a52aaa6e9a9d6780d5f55b6d164db07388e9c595296d4e4a11dc241aa0745fa726279d19a0c97d1966b0a14c06af2b9b588873ad522aeeff881534f0871f10 +DIST biojava-1.7-all.jar 28062592 SHA256 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SHA512 867862b45f014bcd1afd37691e91b948ede05e96f84c7051953d32dad49908781235aad80301e22a15fa8b4145e80c78cf3935d6e581a2e60b56c9308f8adaa8 WHIRLPOOL 5669293ce362e82562454c5902d523e69f64d90e117e75b5de844e0ef5866d250507b86f78245ac82f19932ad9aa196ad17d96a3f703187a3ab2daf00893af9b diff --git a/sci-biology/biojava/biojava-1.6.ebuild b/sci-biology/biojava/biojava-1.6.ebuild new file mode 100644 index 000000000000..edfadace1dcc --- /dev/null +++ b/sci-biology/biojava/biojava-1.6.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-live_${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing budled jars." + find . -name "*.jar" -print -delete + rm -r doc/* + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/biojava-1.7.ebuild b/sci-biology/biojava/biojava-1.7.ebuild new file mode 100644 index 000000000000..77ff74c2d159 --- /dev/null +++ b/sci-biology/biojava/biojava-1.7.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/commons-collections:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing bundled jars..." + find . -name "*.jar" -print -delete + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml new file mode 100644 index 000000000000..0a18364544e8 --- /dev/null +++ b/sci-biology/biojava/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-biology</herd> + <herd>java</herd> +</pkgmetadata> diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest new file mode 100644 index 000000000000..b189a8ae405f --- /dev/null +++ b/sci-biology/bioperl-db/Manifest @@ -0,0 +1 @@ +DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2 diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild new file mode 100644 index 000000000000..b78237d1e434 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-DB +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +SRC_TEST="do" + +CDEPEND=" + >=sci-biology/bioperl-${PV} + dev-perl/DBD-mysql + dev-perl/DBI + sci-biology/biosql" +DEPEND="${CDEPEND} + dev-perl/Module-Build" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild new file mode 100644 index 000000000000..aad5b6e4abe5 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +CDEPEND=">=sci-biology/bioperl-${PV} + dev-perl/DBI + sci-biology/biosql" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-db-${PV}" + +src_configure() { + # This disables tests. TODO: Enable tests + sed -i -e '/biosql_conf();/d' \ + -e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml new file mode 100644 index 000000000000..642468c809b7 --- /dev/null +++ b/sci-biology/bioperl-db/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-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-DB</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest new file mode 100644 index 000000000000..54877a23bece --- /dev/null +++ b/sci-biology/bioperl-network/Manifest @@ -0,0 +1 @@ +DIST BioPerl-Network-1.006900.tar.gz 2198089 SHA256 5b31ab7d048ee8e7bd6ba933f96b904d7ee06b46ab29c00276eca3513a77c32a SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 WHIRLPOOL 65ff9e2509c0136232b7cff1aa5e8ad55f26241f51e70e6d34f9383c0af4bfdb0c5358b1a69075d480e9e1fdfa19342058fbe33ea4d4a633220ef3a80d6ed984 diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild new file mode 100644 index 000000000000..285db499bff4 --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Network +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild new file mode 100644 index 000000000000..5b93a4ddbeed --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-network-${PV}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml new file mode 100644 index 000000000000..045af7cc6148 --- /dev/null +++ b/sci-biology/bioperl-network/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-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-Network</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest new file mode 100644 index 000000000000..bd1970f7c390 --- /dev/null +++ b/sci-biology/bioperl-run/Manifest @@ -0,0 +1 @@ +DIST BioPerl-Run-1.006900.tar.gz 14546677 SHA256 6eddca8aae38a139caaa0b28505e2ff3e919e8ed39b7539a662b0145f1f08d96 SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c WHIRLPOOL a671180b3680d94683e771ba661e0f86430814200efcd8df1552dbc3c30228d90ea8be1b47cc36603cbfc6eadacb276414ae6d79e30ec80495fd836eb1732cca diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild new file mode 100644 index 000000000000..d633fe3be7a1 --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Run +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + dev-perl/File-Sort + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + #find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild new file mode 100644 index 000000000000..13c3ca1477da --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${PV} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-run-${PV}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff new file mode 100644 index 000000000000..5683347a6b52 --- /dev/null +++ b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff @@ -0,0 +1,22 @@ +--- Makefile.PL.original 2003-09-28 23:33:16.000000000 -0400 ++++ Makefile.PL 2003-09-28 23:33:50.000000000 -0400 +@@ -73,19 +73,6 @@ + my $DISTNAME = "bioperl-run"; + my $VERSION = "1.2.2"; + +-my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n'); +-if( $proceed =~ /^[yY]/) { +- my $address = prompt("Enter your email address (no default)",''); +- +- if (open T,">t/pise-email.test") { +-print T "$address\n"; +-close T; +- } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); } +-} else { +- if( -e "t/pise-email.test" ) { +-unlink "t/pise-email.test"; +- } +-} + #$do_autoload_finesse = 0; + #$NAME = 'Bio'; + #$DISTNAME = "GFD"; diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml new file mode 100644 index 000000000000..f8c7078a2813 --- /dev/null +++ b/sci-biology/bioperl-run/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-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-Run</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest new file mode 100644 index 000000000000..756ab900c480 --- /dev/null +++ b/sci-biology/bioperl/Manifest @@ -0,0 +1 @@ +DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild new file mode 100644 index 000000000000..afaa8236b5a2 --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +MY_PN=BioPerl +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.6.901 +inherit perl-module + +SUBPROJECTS="+db +network +run" +MIN_PV=$PV + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" + +REQUIRED_USE="minimal? ( !graphviz )" + +CDEPEND=" + dev-perl/libwww-perl + !minimal? ( + dev-perl/Algorithm-Munkres + dev-perl/Array-Compare + dev-perl/yaml + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Clone + dev-perl/Convert-Binary-C + dev-perl/Data-Stag + dev-perl/GD + dev-perl/Graph + >=dev-perl/HTML-Parser-3.60 + dev-perl/List-MoreUtils + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/set-scalar + dev-perl/SOAP-Lite + dev-perl/Sort-Naturally + dev-perl/Spreadsheet-ParseExcel + >=virtual/perl-Storable-2.05 + >=dev-perl/SVG-2.26 + >=dev-perl/SVG-Graph-0.01 + dev-perl/URI + >=dev-perl/XML-DOM-XPath-0.13 + dev-perl/XML-Parser + >=dev-perl/XML-SAX-0.15 + dev-perl/XML-Simple + dev-perl/XML-Twig + >=dev-perl/XML-Writer-0.4 + dev-perl/XML-DOM + dev-perl/XML-XPath + ) + graphviz? ( dev-perl/GraphViz ) + sqlite? ( dev-perl/DBD-SQLite )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} ) + network? ( >=sci-biology/bioperl-network-${MIN_PV} ) + run? ( >=sci-biology/bioperl-run-${MIN_PV} )" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild new file mode 100644 index 000000000000..1cf70db6b533 --- /dev/null +++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +SUBPROJECTS="+db +network +run" + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/${PN}/${PN}-live.git + https://github.com/${PN}/${PN}-live.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal graphviz ${SUBPROJECTS}" + +CDEPEND=" + dev-perl/Data-Stag + dev-perl/libwww-perl + !minimal? ( + dev-perl/Ace + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Spreadsheet-ParseExcel + dev-perl/Spreadsheet-WriteExcel + >=dev-perl/XML-SAX-0.15 + dev-perl/Graph + dev-perl/SOAP-Lite + dev-perl/Array-Compare + dev-perl/SVG + dev-perl/XML-Simple + dev-perl/XML-Parser + dev-perl/XML-Twig + >=dev-perl/HTML-Parser-3.60 + >=dev-perl/XML-Writer-0.4 + dev-perl/Clone + dev-perl/XML-DOM + dev-perl/set-scalar + dev-perl/XML-XPath + dev-perl/XML-DOM-XPath + dev-perl/Algorithm-Munkres + dev-perl/Data-Stag + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Convert-Binary-C + dev-perl/SVG-Graph + ) + graphviz? ( dev-perl/GraphViz )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) + db? ( >=sci-biology/bioperl-db-${PV} ) + network? ( >=sci-biology/bioperl-network-${PV} ) + run? ( >=sci-biology/bioperl-run-${PV} )" + +S="${WORKDIR}/BioPerl-${PV}" + +src_configure() { + sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ + -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \ + -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \ + || die + if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml new file mode 100644 index 000000000000..210ba364d45f --- /dev/null +++ b/sci-biology/bioperl/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> + <use> + <flag name="run">Install sci-biology/bioperl-run</flag> + <flag name="network">Install sci-biology/bioperl-run</flag> + <flag name="db">Install sci-biology/bioperl-run</flag> + </use> + <upstream> + <remote-id type="cpan">BioPerl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest new file mode 100644 index 000000000000..e835e2490342 --- /dev/null +++ b/sci-biology/biopython/Manifest @@ -0,0 +1 @@ +DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2 diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild new file mode 100644 index 000000000000..9c23f0bd0635 --- /dev/null +++ b/sci-biology/biopython/biopython-1.65.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} pypy ) + +inherit distutils-r1 eutils + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[$(python_gen_usedep 'python*')] + dev-python/networkx[$(python_gen_usedep 'python*')] + dev-python/numpy[$(python_gen_usedep 'python*')] + dev-python/rdflib[$(python_gen_usedep 'python*')] + dev-python/pygraphviz[$(python_gen_usedep 'python2*')] + dev-python/reportlab[$(python_gen_usedep 'python*')] + media-gfx/pydot[$(python_gen_usedep 'python2*')] + " +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch ) + +python_test() { + [[ ${EPYTHON} == pypy ]] && return + cd Tests || die + ${PYTHON} run_tests.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} + +pkg_postinst() { + elog "For database support you need to install:" + optfeature "MySQL" dev-python/mysql-python + optfeature "PostGreSQL" dev-python/psycopg + echo + elog "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +} diff --git a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch new file mode 100644 index 000000000000..2efdef97d799 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch @@ -0,0 +1,40 @@ +From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 +From: Peter Cock <p.j.a.cock@googlemail.com> +Date: Sun, 18 Jan 2015 02:07:54 +0000 +Subject: [PATCH] Clearer error message; update failing test. + +One of the orchid examples now returns different enough +results that the test was failing. The new error message +makes it much easier to pick another positive example to +add to the the white-list. +--- + Tests/test_NCBI_qblast.py | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) + +diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py +index 88bfe61..19f7b35 100644 +--- a/Tests/test_NCBI_qblast.py ++++ b/Tests/test_NCBI_qblast.py +@@ -66,7 +66,7 @@ def test_orchid_est(self): + AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA + GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA + ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""", +- 0.0000001, None, ["21554275", "18409071", "296087288"]) ++ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"]) + + def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits): + try: +@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_ + print("Update this test to have some redundancy...") + for alignment in record.alignments: + print(alignment.hit_id) +- assert found_result, "Missing all of %s in alignments" \ +- % ", ".join(expected_hits) +- self.assertTrue(found_result) ++ self.assertTrue(found_result, ++ "Missing all expected hits (%s), instead have: %s" ++ % (", ".join(expected_hits), ++ ", ".join(a.hit_id for a in record.alignments))) + + # Check the expected result(s) are found in the descriptions + if expected_hits is None: diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/biopython/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/bioruby/Manifest b/sci-biology/bioruby/Manifest new file mode 100644 index 000000000000..9c1f1499ea6f --- /dev/null +++ b/sci-biology/bioruby/Manifest @@ -0,0 +1 @@ +DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7 diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild new file mode 100644 index 000000000000..b50f3fa137fb --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://www.bioruby.org/" +SRC_URI="http://www.${PN}.org/archive/${P}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="amd64 ~ppc x86" + +ruby_add_rdepend "dev-ruby/libxml" + +PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch ) + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/bioruby-9999.ebuild b/sci-biology/bioruby/bioruby-9999.ebuild new file mode 100644 index 000000000000..838f8430c972 --- /dev/null +++ b/sci-biology/bioruby/bioruby-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" +EGIT_REPO_URI="git://github.com/bioruby/bioruby.git + https://github.com/bioruby/bioruby.git" + +inherit git-2 ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://www.bioruby.org/" +SRC_URI="" +SLOT="0" +IUSE="" +KEYWORDS="" + +ruby_add_rdepend "dev-ruby/libxml" + +all_ruby_unpack() { + git-2_src_unpack +} + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch new file mode 100644 index 000000000000..71c4ca27104a --- /dev/null +++ b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch @@ -0,0 +1,29 @@ +From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001 +From: Naohisa Goto <ng@bioruby.org> +Date: Fri, 23 Aug 2013 23:51:59 +0900 +Subject: [PATCH] Test bug fix: Read test file with binary mode to avoid + encoding error + + * Test bug fix: Read test file with binary mode to avoid string encoding + error. Thanks to nieder (github.com/nieder) who reports the bug. + (https://github.com/bioruby/bioruby/issues/84) +--- + test/unit/bio/db/test_phyloxml.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/unit/bio/db/test_phyloxml.rb b/test/unit/bio/db/test_phyloxml.rb +index 0744c64..c24278d 100644 +--- a/test/unit/bio/db/test_phyloxml.rb ++++ b/test/unit/bio/db/test_phyloxml.rb +@@ -100,7 +100,7 @@ def test_open_with_block + end + + def test_new +- str = File.read(TestPhyloXMLData.example_xml) ++ str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read } + assert_instance_of(Bio::PhyloXML::Parser, + phyloxml = Bio::PhyloXML::Parser.new(str)) + common_test_next_tree(phyloxml) +-- +1.8.4 + diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml new file mode 100644 index 000000000000..d4648212cbad --- /dev/null +++ b/sci-biology/bioruby/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/biosql/Manifest b/sci-biology/biosql/Manifest new file mode 100644 index 000000000000..cd5198309e65 --- /dev/null +++ b/sci-biology/biosql/Manifest @@ -0,0 +1 @@ +DIST biosql-1.0.1.tar.bz2 253516 SHA256 3604ceaf6f3e42a11613b49577b7c68f04d9e094cca4e5d932359c815fc9ad01 diff --git a/sci-biology/biosql/biosql-1.0.1.ebuild b/sci-biology/biosql/biosql-1.0.1.ebuild new file mode 100644 index 000000000000..ed77d3770701 --- /dev/null +++ b/sci-biology/biosql/biosql-1.0.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A generic bioinformatics relational database model" +HOMEPAGE="http://www.biosql.org/" +SRC_URI="http://biosql.org/DIST/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +IUSE="mysql postgres" +KEYWORDS="amd64 x86" + +# WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL) + +DEPEND="mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg )" +RDEPEND="${DEPEND}" + +src_install() { + insinto /usr/share/${PN} + doins -r sql scripts/* || die + insinto /usr/share/doc/${P} + doins -r doc/* + dodoc Changes INSTALL README Release.txt +} + +pkg_postinst() { + echo + elog "Please read the BioSQL schema installation instructions in" + elog "/usr/share/doc/${P} to begin using the schema." + echo +} diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/biosql/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/blat/Manifest b/sci-biology/blat/Manifest new file mode 100644 index 000000000000..c1b249e1a095 --- /dev/null +++ b/sci-biology/blat/Manifest @@ -0,0 +1 @@ +DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild new file mode 100644 index 000000000000..c61327420f26 --- /dev/null +++ b/sci-biology/blat/blat-34-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_PN="${PN}Src" + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" + +SLOT="0" +LICENSE="blat" +KEYWORDS="~amd64 ~x86 ~x64-macos" +IUSE="" + +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + sed \ + -e "1i\CFLAGS=${CFLAGS}" \ + -e "1i\LDFLAGS=${LDFLAGS}" \ + -i inc/common.mk || die + tc-export CC +} + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + mkdir -p "${S}/bin/${MACHTYPE}" + emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild new file mode 100644 index 000000000000..41d48bf26bd3 --- /dev/null +++ b/sci-biology/blat/blat-34.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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="amd64 x86" + +MY_PN="${PN}Src" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + sed -i 's/-Werror//; s/CFLAGS=//;' "${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) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch new file mode 100644 index 000000000000..8bdd05bff68d --- /dev/null +++ b/sci-biology/blat/files/34-gentoo.patch @@ -0,0 +1,226 @@ + blat/makefile | 2 +- + gfClient/makefile | 2 +- + gfServer/makefile | 2 +- + hg/pslPretty/makefile | 2 +- + hg/pslReps/makefile | 2 +- + hg/pslSort/makefile | 2 +- + inc/common.mk | 11 +++-------- + makefile | 28 ++++++++++++++-------------- + utils/faToNib/makefile | 2 +- + utils/faToTwoBit/makefile | 2 +- + utils/nibFrag/makefile | 2 +- + utils/twoBitInfo/makefile | 2 +- + utils/twoBitToFa/makefile | 2 +- + 13 files changed, 28 insertions(+), 33 deletions(-) + +diff --git a/blat/makefile b/blat/makefile +index b889c7b..739503a 100644 +--- a/blat/makefile ++++ b/blat/makefile +@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a + O = blat.o + + blat: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/blat${EXE} + + all: +diff --git a/gfClient/makefile b/gfClient/makefile +index c3288de..36e957e 100644 +--- a/gfClient/makefile ++++ b/gfClient/makefile +@@ -8,5 +8,5 @@ O = gfClient.o + X = gfClient + + gfClient: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} +diff --git a/gfServer/makefile b/gfServer/makefile +index c06b3a5..f042d22 100644 +--- a/gfServer/makefile ++++ b/gfServer/makefile +@@ -8,7 +8,7 @@ O = gfServer.o + X = gfServer + + gfServer: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} + + test: +diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile +index c780b96..cbbcd0d 100644 +--- a/hg/pslPretty/makefile ++++ b/hg/pslPretty/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslPretty.o + + pslPretty: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L + + test:: testRna testDnax + +diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile +index 6e8f6d7..2b73b60 100644 +--- a/hg/pslReps/makefile ++++ b/hg/pslReps/makefile +@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslReps.o + + pslReps: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L + + lib: + cd ../../lib && ${MAKE} +diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile +index 81fe083..eb63257 100644 +--- a/hg/pslSort/makefile ++++ b/hg/pslSort/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslSort.o + + pslSort: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L + + + lib: +diff --git a/inc/common.mk b/inc/common.mk +index 1823163..3a04e2b 100644 +--- a/inc/common.mk ++++ b/inc/common.mk +@@ -1,20 +1,15 @@ +-CC=gcc +-ifeq (${COPT},) +- COPT=-O +-endif +-CFLAGS= + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} + HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type + HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc + + # Stronger warning checks, and warnings-->errors, for libraries and CGIs: + ifeq (darwin,$(findstring darwin,${OSTYPE})) +- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable ++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable + else + ifeq (solaris,$(findstring solaris,${OSTYPE})) + HG_WARN_ERR = -DJK_WARN -Wall + else +- HG_WARN_ERR = -DJK_WARN -Wall -Werror ++ HG_WARN_ERR = -DJK_WARN -Wall + endif + endif + # Apply the stronger checks to all code on our development machine: +@@ -37,7 +32,7 @@ ifeq (${BINDIR},) + endif + MKDIR=mkdir -p + ifeq (${STRIP},) +- STRIP=strip ++ STRIP=true + endif + CVS=cvs + +diff --git a/makefile b/makefile +index 6f9fddf..dded1cd 100644 +--- a/makefile ++++ b/makefile +@@ -1,18 +1,18 @@ + all: +- cd lib && ${MAKE} +- cd jkOwnLib && ${MAKE} +- cd blat && $(MAKE) +- cd gfClient && $(MAKE) +- cd gfServer && $(MAKE) +- cd hg/pslPretty && $(MAKE) +- cd hg/pslReps && $(MAKE) +- cd hg/pslSort && $(MAKE) +- cd utils/nibFrag && $(MAKE) +- cd utils/faToNib && $(MAKE) +- cd utils/faToTwoBit && $(MAKE) +- cd utils/twoBitToFa && $(MAKE) +- cd utils/twoBitInfo && $(MAKE) +- cd webBlat && $(MAKE) ++ $(MAKE) -C lib ++ $(MAKE) -C jkOwnLib ++ $(MAKE) -C blat ++ $(MAKE) -C gfClient ++ $(MAKE) -C gfServer ++ $(MAKE) -C hg/pslPretty ++ $(MAKE) -C hg/pslReps ++ $(MAKE) -C hg/pslSort ++ $(MAKE) -C utils/nibFrag ++ $(MAKE) -C utils/faToNib ++ $(MAKE) -C utils/faToTwoBit ++ $(MAKE) -C utils/twoBitToFa ++ $(MAKE) -C utils/twoBitInfo ++ $(MAKE) -C webBlat + + clean: + rm -f */*.o */*/*.o +diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile +index fd0e3eb..63a1593 100644 +--- a/utils/faToNib/makefile ++++ b/utils/faToNib/makefile +@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = faToNib.o + + faToNib: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L +diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile +index b1b44a9..1e8c1c8 100644 +--- a/utils/faToTwoBit/makefile ++++ b/utils/faToTwoBit/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = faToTwoBit.o + + faToTwoBit: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/faToTwoBit${EXE} + + clean: +diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile +index 260a6f3..e37b9ab 100755 +--- a/utils/nibFrag/makefile ++++ b/utils/nibFrag/makefile +@@ -4,7 +4,7 @@ include ../../inc/common.mk + O = nibFrag.o + + nibFrag: $(O) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a + + + +diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile +index 649784f..9434d1c 100644 +--- a/utils/twoBitInfo/makefile ++++ b/utils/twoBitInfo/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = twoBitInfo.o + + twoBitInfo: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/twoBitInfo${EXE} + + clean: +diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile +index cf979f2..081f3b8 100644 +--- a/utils/twoBitToFa/makefile ++++ b/utils/twoBitToFa/makefile +@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = twoBitToFa.o + + twoBitToFa: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L + #${STRIP} ${BINDIR}/twoBitToFa${EXE} + + clean: diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /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>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest new file mode 100644 index 000000000000..96859ca6bf5f --- /dev/null +++ b/sci-biology/blossoc/Manifest @@ -0,0 +1 @@ +DIST blossoc-1.4.0.tar.gz 194885 SHA256 b23f51349f72f31263b8aca162c7590a5f52b72fd5e0d91b4a2591098ff5bdbe diff --git a/sci-biology/blossoc/blossoc-1.4.0.ebuild b/sci-biology/blossoc/blossoc-1.4.0.ebuild new file mode 100644 index 000000000000..7e5b6694d395 --- /dev/null +++ b/sci-biology/blossoc/blossoc-1.4.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit autotools eutils + +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/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="sci-libs/gsl + dev-libs/boost + sci-biology/snpfile" +RDEPEND="${DEPEND}" + +src_prepare() { + sed -i '/TESTS += first_test.sh/ d' "${S}/Makefile.am" || die + epatch "${FILESDIR}"/${P}-gcc43.patch + eautoreconf +} + +src_install() { + emake install DESTDIR="${D}" || die "emake install failed" +} diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch new file mode 100644 index 000000000000..d8e354c1745f --- /dev/null +++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch @@ -0,0 +1,15 @@ +Fixes build with >=GCC-4.3 + +http://bugs.gentoo.org/show_bug.cgi?id=292949 + +Patch written by Sebastian Luther <SebastianLuther@gmx.de> +--- pph.cc ++++ pph.cc +@@ -23,6 +23,7 @@ + */ + + #include "pph.hh" ++#include <cstdio> + #include <cmath> + #include <snpfile/matrix.hh> + using namespace BiRC::SNPFile; diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /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>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest new file mode 100644 index 000000000000..1345a9e07e4e --- /dev/null +++ b/sci-biology/bowtie/Manifest @@ -0,0 +1,2 @@ +DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 +DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1 diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild new file mode 100644 index 000000000000..c26c986ed194 --- /dev/null +++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) +# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-47.patch +} + +src_compile() { + unset CFLAGS + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL +} diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild new file mode 100644 index 000000000000..b8181190243c --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.0.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_compile() { + unset CFLAGS + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + + insinto /usr/share/${PN} + doins -r genomes indexes + + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL doc/README + dohtml doc/{manual.html,style.css} +} diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch new file mode 100644 index 000000000000..3c8a1e1d9ca4 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch @@ -0,0 +1,45 @@ + alphabet.h | 24 ++++++++++++------------ + 1 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/alphabet.h b/alphabet.h +index b464ddf..08d0281 100644 +--- a/alphabet.h ++++ b/alphabet.h +@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { + return s_rc; + } + ++/// Reverse a string in-place ++template <typename TStr> ++static inline void reverseInPlace(TStr& s) { ++ typedef typename Value<TStr>::Type TVal; ++ size_t len = length(s); ++ for(size_t i = 0; i < (len>>1); i++) { ++ TVal tmp = s[i]; ++ s[i] = s[len-i-1]; ++ s[len-i-1] = tmp; ++ } ++} ++ + /** + * Reverse-complement s in-place. Ns go to Ns. + */ +@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { + } + } + +-/// Reverse a string in-place +-template <typename TStr> +-static inline void reverseInPlace(TStr& s) { +- typedef typename Value<TStr>::Type TVal; +- size_t len = length(s); +- for(size_t i = 0; i < (len>>1); i++) { +- TVal tmp = s[i]; +- s[i] = s[len-i-1]; +- s[len-i-1] = tmp; +- } +-} +- + /** + * Return the reverse-complement of s. + */ diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml new file mode 100644 index 000000000000..e493417070fb --- /dev/null +++ b/sci-biology/bowtie/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-biology</herd> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000000..9c0d995bfb1f --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1 @@ +DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild new file mode 100644 index 000000000000..76ed0cca912b --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.12.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" +HOMEPAGE="http://bio-bwa.sourceforge.net/" +SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~x64-macos" + +PATCHES=( "${FILESDIR}"/${P}-Makefile.patch ) + +src_prepare() { + epatch ${PATCHES[@]} + tc-export CC AR +} + +src_install() { + dobin bwa + + doman bwa.1 + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + dodoc NEWS.md README-alt.md README.md +} diff --git a/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch new file mode 100644 index 000000000000..406e9b052376 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch @@ -0,0 +1,27 @@ +--- Makefile ++++ Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o + AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -26,10 +26,10 @@ + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml new file mode 100644 index 000000000000..97a33fbf5c42 --- /dev/null +++ b/sci-biology/bwa/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-biology</herd> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest new file mode 100644 index 000000000000..c3cf3842c604 --- /dev/null +++ b/sci-biology/cd-hit/Manifest @@ -0,0 +1,3 @@ +DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 +DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 RMD160 00fca8d2527a4a6b1eda861f8f750e10ee565ae7 SHA1 743c4b6ec79b9d5acd1e1171587e96c03e3e3003 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a +DIST cd-hit-v4.6-2012-04-25.tgz 652228 RMD160 318239a9416fd3cd57754546c8fcc0a4cea7f5d8 SHA1 e47c662c0a284ae99e47205d6a4eaea805a76cae SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild new file mode 100644 index 000000000000..d47948f0d821 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2011-01-31" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} || die +} + +src_install() { + dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die + dodoc ChangeLog cdhit-user-guide.pdf || die +} diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild new file mode 100644 index 000000000000..bafa3301d724 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2011-03-07" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} +} + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}/usr/bin" install + dodoc ChangeLog cdhit-user-guide.pdf +} diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild new file mode 100644 index 000000000000..d7dd15559c5c --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.6.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2012-04-25" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="doc openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} +} + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}/usr/bin" install + dodoc ChangeLog + use doc && dodoc doc/* +} diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch new file mode 100644 index 000000000000..c3eaf79cc8f2 --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch @@ -0,0 +1,85 @@ +diff --git a/Makefile b/Makefile +index f1eaa26..92d3130 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,39 +37,39 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch new file mode 100644 index 000000000000..5aa9b79e02ae --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.4-gentoo.patch @@ -0,0 +1,98 @@ + Makefile | 36 ++++++++++++++++++------------------ + 1 files changed, 18 insertions(+), 18 deletions(-) + +diff --git a/Makefile b/Makefile +index e8bac1d..bd31093 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,47 +37,47 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c + + PREFIX ?= /usr/local/bin + diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch new file mode 100644 index 000000000000..7a376eb8e73c --- /dev/null +++ b/sci-biology/cd-hit/files/4.6-gentoo.patch @@ -0,0 +1,117 @@ + Makefile | 47 ++++++++++++++++++++++------------------------- + 1 files changed, 22 insertions(+), 25 deletions(-) + +diff --git a/Makefile b/Makefile +index e9796a1..97dd72b 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,16 +1,13 @@ +- +-CC = g++ -Wall -ggdb +-CC = g++ -pg +-CC = g++ ++CXX ?= g++ + + # without OpenMP +-CCFLAGS = -DNO_OPENMP ++#CXXFLAGS = -DNO_OPENMP + + # with OpenMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,22 +15,22 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += + else +-CCFLAGS += -O2 ++CXXFLAGS += + endif + + ifdef MAX_SEQ +-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ) ++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ) + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++#LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -43,47 +40,47 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c + + PREFIX ?= /usr/local/bin + diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml new file mode 100644 index 000000000000..bd5607ab16b5 --- /dev/null +++ b/sci-biology/cd-hit/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> +CD-HIT is a very widely used program for clustering and comparing large sets +of protein or nucleotide sequences. CD-HIT is very fast and can handle +extremely large databases. CD-HIT helps to significantly reduce the +computational and manual efforts in many sequence analysis tasks and aids in +understanding the data structure and correct the bias within a dataset. +The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, +CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT +(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a +user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 +datasets and identifies the sequences in db2 that are similar to db1 above +a threshold. CD-HIT-454 is a program to identify natural and artificial +duplicates from pyrosequencing reads. The usage of other programs and +scripts can be found in CD-HIT user's guide. +</longdescription> + <upstream> + <remote-id type="google-code">cdhit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest new file mode 100644 index 000000000000..2394b3a452f6 --- /dev/null +++ b/sci-biology/clustal-omega/Manifest @@ -0,0 +1,2 @@ +DIST clustal-omega-1.2.0.tar.gz 1156741 SHA256 cbf5ad4e1ce88641cca307be1edfe95d3882997d71c11b43c8e1fcd6e388c61d SHA512 d207699e1158178e2d7122620026b199251ab86bcc3f72a08d58f23e2dd5c2961340e872a13c34f1d6832c5eef5ff8ab09c43f0cb51a81d6c4ef554f936434e2 WHIRLPOOL 41505b42829d440fd312f1538ef78fb7d0f668008cd00bcc52022139eb2ff21d05d89519af2a18e5a2f845e24a5d374a81eb4163c2720a32f71ead7ce40e4eac +DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256 0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512 1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de WHIRLPOOL b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577 diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild new file mode 100644 index 000000000000..ccded19116cd --- /dev/null +++ b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Scalable multiple alignment of protein sequences" +HOMEPAGE="http://www.clustal.org/omega/" +SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND="dev-libs/argtable" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_prepare() { + sed \ + -e "s:-O3::g" \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die + fi +} diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild new file mode 100644 index 000000000000..e56766f9416e --- /dev/null +++ b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Scalable multiple alignment of protein sequences" +HOMEPAGE="http://www.clustal.org/omega/" +SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND="dev-libs/argtable" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_prepare() { + sed \ + -e "s:-O3::g" \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die + fi +} diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustal-omega/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/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest new file mode 100644 index 000000000000..b1f7bb630cd0 --- /dev/null +++ b/sci-biology/clustalw-mpi/Manifest @@ -0,0 +1 @@ +DIST clustalw-mpi-0.13.tar.gz 154911 RMD160 9da3e418efcb0cfd0c5df2705ee217b9dacc3917 SHA1 ae5026e8b4ba58bb0caa5643ea90434d9589df5a SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845 diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild new file mode 100644 index 000000000000..11f1e57e2731 --- /dev/null +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm" +HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" +SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="public-domain" +IUSE="mpi_njtree static_pairalign" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + if use mpi_njtree; then + sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ + die "Failed to configure MPI code for NJ trees." + fi + if use static_pairalign; then + sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ + die "Failed to configure static scheduling for pair alignments." + fi +} + +src_install() { + dobin ${PN} + newdoc README.${PN} README +} diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch new file mode 100644 index 000000000000..6e36061cbb39 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch @@ -0,0 +1,23 @@ + Makefile | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index f2107ce..835232b 100644 +--- a/Makefile ++++ b/Makefile +@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE + PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN + #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN + +-CFLAGS = -c -O3 ++CFLAGS += -c + #CFLAGS = -c -O3 -funroll-all-loops +-LFLAGS = -lm ++LIBS = -lm + + clustalw-mpi: $(OBJECTS) +- $(CC) -o $@ $(OBJECTS) $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml new file mode 100644 index 000000000000..905eba1a07b8 --- /dev/null +++ b/sci-biology/clustalw-mpi/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-biology</herd> +<use> + <flag name='mpi_njtree'>Use MPI (as opposed to serial) code for computing + neighbor-joining trees</flag> + <flag name='static_pairalign'>Use static (as opposed to dynamic) scheduling + for pair alignments</flag> +</use> +</pkgmetadata> diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest new file mode 100644 index 000000000000..7d1b7dca8a7f --- /dev/null +++ b/sci-biology/clustalw/Manifest @@ -0,0 +1,2 @@ +DIST clustalw-2.1.tar.gz 350761 SHA256 e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921 WHIRLPOOL 93158f400cbdf11ecddcac15b5b4cee9af61d9b933f7100ad18d01d346de54c6bad5a9a12fe5a70a265c92581d3ee9cfbc41b17ee2c2ff80ff2a6658efba5f40 +DIST clustalw1.83.UNIX.tar.gz 166863 SHA256 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60 SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a WHIRLPOOL 5a075579737d8a9ba5f62d6f90feb53a275bd31a8131d1b7d21395cf46cfefbdf4e48563b55734c995b9e3d8f9c37c78ea77f4e48920d64781190645ea36112b diff --git a/sci-biology/clustalw/clustalw-1.83-r3.ebuild b/sci-biology/clustalw/clustalw-1.83-r3.ebuild new file mode 100644 index 000000000000..6047a08ed466 --- /dev/null +++ b/sci-biology/clustalw/clustalw-1.83-r3.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" + +LICENSE="clustalw" +SLOT="1" +KEYWORDS="alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" + +S="${WORKDIR}"/${PN}${PV} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + + sed \ + -e "/^CC/s:cc:$(tc-getCC):g" \ + -i makefile || die + sed \ + -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -i clustalw.c || die +} + +src_install() { + dobin clustalw + dodoc README clustalv.doc clustalw.doc clustalw.ms + insinto /usr/share/doc/${PF} + doins clustalw_help +} diff --git a/sci-biology/clustalw/clustalw-2.1.ebuild b/sci-biology/clustalw/clustalw-2.1.ebuild new file mode 100644 index 000000000000..8664ee3108ec --- /dev/null +++ b/sci-biology/clustalw/clustalw-2.1.ebuild @@ -0,0 +1,14 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.clustal.org/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch new file mode 100644 index 000000000000..62b4654cddea --- /dev/null +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -0,0 +1,17 @@ +--- makefile 2003-01-29 09:53:45.000000000 +0100 ++++ makefile.new 2009-08-17 08:33:16.000000000 +0200 +@@ -11,11 +11,11 @@ + HEADERS = general.h clustalw.h + + CC = cc +-CFLAGS = -c -O +-LFLAGS = -O -lm ++CFLAGS += -c ++LIBS = -lm + + clustalw : $(OBJECTS) amenu.o clustalw.o +- $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustalw/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/clustalx/Manifest b/sci-biology/clustalx/Manifest new file mode 100644 index 000000000000..acbf2db29963 --- /dev/null +++ b/sci-biology/clustalx/Manifest @@ -0,0 +1 @@ +DIST clustalx-2.1.tar.gz 341649 SHA256 e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 WHIRLPOOL 6cbe8dcf2be3a535e8ac0ef0b9b476d4429a80bd94b394c0194f46ed039f9ac2b97b0ec2ed680838a0973b3187b2dbc90285733657975e03288b9840ba3d6b15 diff --git a/sci-biology/clustalx/clustalx-2.1-r1.ebuild b/sci-biology/clustalx/clustalx-2.1-r1.ebuild new file mode 100644 index 000000000000..9aa885eaa5bb --- /dev/null +++ b/sci-biology/clustalx/clustalx-2.1-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils qt4-r2 + +DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" +HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4" +RDEPEND="${DEPEND} + >=sci-biology/clustalw-${PV}" + +src_prepare() { + sed \ + -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \ + -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \ + -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \ + -i ClustalQtParams.h || \ + die "Failed to patch shared files location." + sed \ + -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ + -i HelpDisplayWidget.cpp || \ + die "Failed to patch help file location." + rm -rf usr || die +} + +src_install() { + dobin clustalx + insinto /usr/share/${PN} + doins colprot.xml coldna.xml colprint.xml clustalx.hlp + make_desktop_entry ${PN} ClustalX +} diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustalx/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/consed/Manifest b/sci-biology/consed/Manifest new file mode 100644 index 000000000000..e9cd6b128266 --- /dev/null +++ b/sci-biology/consed/Manifest @@ -0,0 +1,4 @@ +DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089 +DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3 +DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 +DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild new file mode 100644 index 000000000000..3ce704e8792f --- /dev/null +++ b/sci-biology/consed/consed-19-r2.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI="${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=x11-libs/motif-2.3:0" +RDEPEND="${DEPEND} + >=sci-biology/phred-000925 + >=sci-biology/phrap-1.080721" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die + sed -i \ + -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \ + -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ + -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die + sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die + sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${PN}/examples + doins -r standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer || die + echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + doenvd "${S}/99consed" || die + dodoc README.txt *_announcement.txt || die +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild new file mode 100644 index 000000000000..0bf33a7278cf --- /dev/null +++ b/sci-biology/consed/consed-27.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI=" + ${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=x11-libs/motif-2.3:0" +RDEPEND="${DEPEND} + sci-biology/samtools + >=sci-biology/phred-000925 + >=sci-biology/phrap-1.080721 + dev-lang/perl" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die + sed -i \ + -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ + -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ + -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ + -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die + sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die + sed \ + -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \ + -i "${S}"/scripts/* || die +} + +src_compile() { + emake + emake -C misc/mktrace + emake -C misc/phd2fasta + (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} + dobin scripts/* contributions/* + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + insinto /usr/share/${PN}/examples + doins -r \ + standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer + echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die + echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die + mkdir -p "${ED}"/etc/consedrc || die + touch "${ED}"/etc/consedrc || die + doenvd "${S}/99consed" || die + sed \ + -e "s#/usr/local/genome#${EPREFIX}/usr#" \ + -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die + sed \ + -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \ + -i "${ED}"/usr/bin/phredPhrap || die + sed \ + -e 's#/wt1/gordon/genome#/usr/bin#' \ + -i "${ED}"/usr/bin/fastq2Phrap.perl || die + dodoc README.txt *_announcement.txt || die +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/consed/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/cufflinks/Manifest b/sci-biology/cufflinks/Manifest new file mode 100644 index 000000000000..017836ee07ad --- /dev/null +++ b/sci-biology/cufflinks/Manifest @@ -0,0 +1,2 @@ +DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce +DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224 diff --git a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild new file mode 100644 index 000000000000..36322f463de6 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=sci-biology/samtools-0.1.18 + <sci-biology/samtools-1 + <dev-libs/boost-1.56:=" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-boost.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + ) + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild new file mode 100644 index 000000000000..66298cbc1972 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils flag-o-matic toolchain-funcs + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + || ( + ( + >=sci-biology/samtools-0.1.18 + sci-libs/htslib + ) + <sci-biology/samtools-1 + ) + >=dev-libs/boost-1.47.0:= + <dev-libs/boost-1.56.0:= + dev-cpp/eigen:3 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-hts.patch + "${FILESDIR}"/${P}-flags.patch + ) + +src_prepare() { + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/cufflinks-2.2.1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild new file mode 100644 index 000000000000..5e7f763389f9 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools-utils flag-o-matic toolchain-funcs + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=sci-biology/samtools-0.1.18 + <sci-biology/samtools-1 + >=dev-libs/boost-1.47.0:= + <dev-libs/boost-1.56.0:= + dev-cpp/eigen:3 +" +RDEPEND="${DEPEND}" + +src_prepare() { + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch new file mode 100644 index 000000000000..73e52b4343a0 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch @@ -0,0 +1,38 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -27,6 +27,7 @@ AC_PROG_AWK + AC_PROG_CXX + AC_PROG_CC + AC_PROG_MAKE_SET ++AM_PROG_AR + AC_PROG_RANLIB + AC_PROG_INSTALL + AM_PATH_PYTHON([2.4]) +@@ -54,7 +55,7 @@ AC_CANONICAL_HOST + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized" + ext_CFLAGS="" + debug_CFLAGS="" + #echo "${host_cpu}-${host_os}" +@@ -99,15 +100,15 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS" ++CXXFLAGS="$CXXFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++LDFLAGS="$LDFLAGS $ext_LDFLAGS" + + # Checks for structures/functions that can be used to determine system memory + AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>]) + AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>]) + +-AM_INIT_AUTOMAKE([-Wall -Werror tar-pax foreign]) ++AM_INIT_AUTOMAKE([-Wall tar-pax foreign subdir-objects]) + + AC_CONFIG_FILES([Makefile + src/Makefile]) diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch new file mode 100644 index 000000000000..d45391bf4f3a --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch @@ -0,0 +1,1320 @@ + ax_boost_thread.m4 | 6 +++--- + src/abundances.cpp | 56 +++++++++++++++++++++++++------------------------- + src/biascorrection.cpp | 2 +- + src/bundles.cpp | 10 ++++----- + src/bundles.h | 10 ++++----- + src/common.h | 4 ++-- + src/compress_gtf.cpp | 12 +++++------ + src/cuffdiff.cpp | 30 +++++++++++++-------------- + src/cufflinks.cpp | 34 +++++++++++++++--------------- + src/differential.cpp | 38 +++++++++++++++++----------------- + src/filters.cpp | 8 ++++---- + src/genes.h | 6 +++--- + src/gtf_to_sam.cpp | 8 ++++---- + src/hits.cpp | 4 ++-- + src/replicates.cpp | 6 +++--- + src/replicates.h | 18 ++++++++-------- + src/scaffolds.cpp | 28 ++++++++++++------------- + src/scaffolds.h | 2 +- + 18 files changed, 141 insertions(+), 141 deletions(-) + +diff --git a/ax_boost_thread.m4 b/ax_boost_thread.m4 +index d1d42f6..6f99f1b 100644 +--- a/ax_boost_thread.m4 ++++ b/ax_boost_thread.m4 +@@ -105,20 +105,20 @@ AC_DEFUN([AX_BOOST_THREAD], + for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + if test "x$link_thread" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + fi + + else +- BOOST_THREAD_LIB="$ax_boost_user_thread_lib"; ++ BOOST_THREAD_LIB="$ax_boost_user_thread_lib -lboost_system"; + AC_SUBST(BOOST_THREAD_LIB) + link_thread="yes"; + +diff --git a/src/abundances.cpp b/src/abundances.cpp +index d8f81d0..6e717dc 100644 +--- a/src/abundances.cpp ++++ b/src/abundances.cpp +@@ -140,7 +140,7 @@ AbundanceStatus AbundanceGroup::status() const + { + bool has_lowdata_member = false; + bool has_ok_member = false; +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + if (ab->status() == NUMERIC_FAIL) + { +@@ -205,7 +205,7 @@ void TranscriptAbundance::FPKM_variance(double v) + + bool AbundanceGroup::has_member_with_status(AbundanceStatus member_status) + { +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + if (ab->status() == member_status) + { +@@ -219,7 +219,7 @@ double AbundanceGroup::num_fragments() const + { + double num_f = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + num_f += ab->num_fragments(); + } +@@ -231,7 +231,7 @@ double AbundanceGroup::mass_fraction() const + { + double mass = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + mass += ab->mass_fraction(); + } +@@ -242,7 +242,7 @@ double AbundanceGroup::mass_variance() const + { + double mass_var = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + mass_var += ab->mass_variance(); + } +@@ -253,7 +253,7 @@ double AbundanceGroup::FPKM() const + { + double fpkm = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + fpkm += ab->FPKM(); + } +@@ -265,7 +265,7 @@ double AbundanceGroup::gamma() const + { + double gamma = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + gamma += ab->gamma(); + } +@@ -281,7 +281,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep, + assert (to_keep.size() == _abundances.size()); + + size_t num_kept = 0; +- foreach(bool keeper, to_keep) ++ for_each(bool keeper, to_keep) + { + num_kept += keeper; + } +@@ -331,7 +331,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep, + void AbundanceGroup::get_transfrags(vector<shared_ptr<Abundance> >& transfrags) const + { + transfrags.clear(); +- foreach(shared_ptr<Abundance> pA, _abundances) ++ for_each(shared_ptr<Abundance> pA, _abundances) + { + shared_ptr<Scaffold> pS = pA->transfrag(); + if (pS) +@@ -345,7 +345,7 @@ set<string> AbundanceGroup::gene_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->gene_id(); + s.insert(sub.begin(), sub.end()); +@@ -358,7 +358,7 @@ set<string> AbundanceGroup::gene_name() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->gene_name(); + s.insert(sub.begin(), sub.end()); +@@ -372,7 +372,7 @@ set<string> AbundanceGroup::tss_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->tss_id(); + s.insert(sub.begin(), sub.end()); +@@ -385,7 +385,7 @@ set<string> AbundanceGroup::protein_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->protein_id(); + s.insert(sub.begin(), sub.end()); +@@ -398,7 +398,7 @@ const string& AbundanceGroup::locus_tag() const + { + static string default_locus_tag = "-"; + const string* pLast = NULL; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pLast) + { +@@ -422,7 +422,7 @@ const string& AbundanceGroup::reference_tag() const + { + static string default_reference_tag = "-"; + const string* pLast = NULL; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pLast) + { +@@ -448,7 +448,7 @@ double AbundanceGroup::effective_length() const + double group_fpkm = FPKM(); + if (group_fpkm == 0) + return 0; +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + eff_len += (ab->effective_length() * (ab->FPKM() / group_fpkm)); + } +@@ -1216,7 +1216,7 @@ void AbundanceGroup::estimate_count_covariance() + { + // if the entire group is unstable, then set LOWDATA on all members of + // it to reduce false positives in differential expression analysis. +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + ab->status(NUMERIC_LOW_DATA); + } +@@ -1468,7 +1468,7 @@ void AbundanceGroup::calculate_conf_intervals() + double sum_transfrag_FPKM_hi = 0; + double max_fpkm = 0.0; + //double min_fpkm = 1e100; +- foreach(shared_ptr<Abundance> pA, _abundances) ++ for_each(shared_ptr<Abundance> pA, _abundances) + { + double FPKM_hi; + double FPKM_lo; +@@ -1586,7 +1586,7 @@ void AbundanceGroup::calculate_conf_intervals() + // double sum_transfrag_FPKM_hi = 0; + // double max_fpkm = 0.0; + // //double min_fpkm = 1e100; +-// foreach(shared_ptr<Abundance> pA, _abundances) ++// for_each(shared_ptr<Abundance> pA, _abundances) + // { + // double FPKM_hi; + // double FPKM_lo; +@@ -1732,7 +1732,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments, + if (mapped_transcripts.empty()) + { + //gammas = vector<double>(transfrags.size(), 0.0); +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + ab->gamma(0); + } +@@ -1783,7 +1783,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments, + if (filtered_transcripts.empty()) + { + //gammas = vector<double>(transfrags.size(), 0.0); +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + ab->gamma(0); + } +@@ -2117,7 +2117,7 @@ void AbundanceGroup::calculate_kappas() + double S_FPKM = 0.0; + double Z_kappa = 0.0; + double X_S = 0.0; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pA->effective_length() > 0) + { +@@ -2128,7 +2128,7 @@ void AbundanceGroup::calculate_kappas() + } + + //fprintf (stderr, "*********\n"); +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (S_FPKM > 0) + { +@@ -2201,7 +2201,7 @@ void get_alignments_from_scaffolds(const vector<shared_ptr<Abundance> >& abundan + { + set<const MateHit*> hits_in_gene_set; + +- foreach(shared_ptr<Abundance> pA, abundances) ++ for_each(shared_ptr<Abundance> pA, abundances) + { + shared_ptr<Scaffold> pS = pA->transfrag(); + assert (pS); +@@ -2787,7 +2787,7 @@ AbundanceStatus empirical_mean_replicate_gamma_mle(const vector<shared_ptr<Abund + gamma_covariance = ublas::zero_matrix<double>(N,N); + ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N); + // +- foreach(ublas::vector<double>& mle, mle_gammas) ++ for_each(ublas::vector<double>& mle, mle_gammas) + { + expected_mle_gamma += mle; + } +@@ -3122,7 +3122,7 @@ AbundanceStatus bootstrap_gamma_mle(const vector<shared_ptr<Abundance> >& transc + gamma_covariance = ublas::zero_matrix<double>(N,N); + ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N); + +- foreach(ublas::vector<double>& mle, mle_gammas) ++ for_each(ublas::vector<double>& mle, mle_gammas) + { + //cerr << "MLE # "<< MLENUM++ << endl; + //cerr << mle << endl; +@@ -3586,7 +3586,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts, + + double round_err = 0.0; + double num_good = 0; +- foreach (double& g, gammas) ++ for_each (double& g, gammas) + { + if (g < min_isoform_fraction) + { +@@ -3598,7 +3598,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts, + num_good += 1; + } + } +- foreach (double& g, gammas) ++ for_each (double& g, gammas) + { + if (g != 0) + { +diff --git a/src/biascorrection.cpp b/src/biascorrection.cpp +index 0d49851..55884f4 100644 +--- a/src/biascorrection.cpp ++++ b/src/biascorrection.cpp +@@ -207,7 +207,7 @@ void BiasLearner::preProcessTranscript(const Scaffold& transcript) + vector<double> startHist(transcript.length()+1, 0.0); // +1 catches overhangs + vector<double> endHist(transcript.length()+1, 0.0); + +- foreach (const MateHit* hit_p, transcript.mate_hits()) ++ for_each (const MateHit* hit_p, transcript.mate_hits()) + { + const MateHit& hit = *hit_p; + if (!hit.left_alignment() && !hit.right_alignment()) +diff --git a/src/bundles.cpp b/src/bundles.cpp +index ead07f2..a392514 100644 +--- a/src/bundles.cpp ++++ b/src/bundles.cpp +@@ -228,7 +228,7 @@ void load_ref_rnas(FILE* ref_mRNA_file, + } + } + +- foreach (shared_ptr<Scaffold> s, ref_mRNAs) ++ for_each (shared_ptr<Scaffold> s, ref_mRNAs) + { + assert (s); + } +@@ -418,7 +418,7 @@ void HitBundle::finalize_open_mates() + + for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr) + { +- foreach (MateHit& hit, itr->second) ++ for_each (MateHit& hit, itr->second) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -438,7 +438,7 @@ void HitBundle::remove_hitless_scaffolds() + void HitBundle::remove_unmapped_hits() + { + +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + if (unmapped_hit(hit)) + { +@@ -586,7 +586,7 @@ void HitBundle::finalize(bool is_combined) + } + else + { +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + hit.incr_collapse_mass(hit.common_scale_mass()); + } +@@ -1316,7 +1316,7 @@ void identify_bad_splices(const HitBundle& bundle, + ins_itr = bad_splice_ops.insert(make_pair(ref_id, vector<AugmentedCuffOp>())); + vector<AugmentedCuffOp>& bad_introns = ins_itr.first->second; + +- foreach (const MateHit& hit, bundle.hits()) ++ for_each (const MateHit& hit, bundle.hits()) + { + if (hit.left_alignment()) + { +diff --git a/src/bundles.h b/src/bundles.h +index 15f51ee..aec725e 100644 +--- a/src/bundles.h ++++ b/src/bundles.h +@@ -57,7 +57,7 @@ public: + ~HitBundle() + { + vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds(); +- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) ++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) + { + // This bundle and the factory that actually owns the ref_mRNAs + // are the only objects that should have access to these scaffolds +@@ -73,7 +73,7 @@ public: + } + } + +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -81,7 +81,7 @@ public: + + for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr) + { +- foreach (MateHit& hit, itr->second) ++ for_each (MateHit& hit, itr->second) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -113,7 +113,7 @@ public: + _hits.clear(); + _non_redundant.clear(); + vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds(); +- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) ++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) + { + if (ref_scaff.use_count() <= 3) + { +@@ -250,7 +250,7 @@ public: + next_ref_scaff = ref_mRNAs.begin(); + next_mask_scaff = mask_gtf_recs.begin(); + +- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) ++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) + { + ref_scaff->clear_hits(); + } +diff --git a/src/common.h b/src/common.h +index b715e9c..1ed7d77 100644 +--- a/src/common.h ++++ b/src/common.h +@@ -22,8 +22,8 @@ + using boost::math::normal; + + #include <boost/foreach.hpp> +-#define foreach BOOST_FOREACH +-#define reverse_foreach BOOST_REVERSE_FOREACH ++#define for_each BOOST_FOREACH ++#define reverse_for_each BOOST_REVERSE_FOREACH + + #include <boost/thread.hpp> + #include <boost/shared_ptr.hpp> +diff --git a/src/compress_gtf.cpp b/src/compress_gtf.cpp +index a2cd10a..a3796fd 100644 +--- a/src/compress_gtf.cpp ++++ b/src/compress_gtf.cpp +@@ -159,7 +159,7 @@ void compress_genes(FILE* ftranscripts, + vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i]; + vector<Scaffold> gene_scaffs; + string gene_id; +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + if (gene_id == "") + gene_id = s->annotated_gene_id(); +@@ -175,7 +175,7 @@ void compress_genes(FILE* ftranscripts, + Scaffold smashed_gene; + if (!proj_intersection && !proj_union) + { +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + /* + *transfrag, +@@ -224,7 +224,7 @@ void compress_genes(FILE* ftranscripts, + int gmax = -1; + int gmin = numeric_limits<int>::max(); + +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + //iso_ops.push_back(s->augmented_ops()); + //sort (iso_ops.back().begin(), iso_ops.back().end()); +@@ -234,7 +234,7 @@ void compress_genes(FILE* ftranscripts, + gmax = s->right(); + } + +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + if (s->left() > gmin) + { +@@ -347,7 +347,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* gtf_out) + vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table; + vector<pair<string, vector<double> > > sample_count_table; + +- foreach (FILE* ref_gtf, ref_gtf_files) ++ for_each (FILE* ref_gtf, ref_gtf_files) + { + vector<shared_ptr<Scaffold> > ref_mRNAs; + ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true); +@@ -393,7 +393,7 @@ int main(int argc, char** argv) + + vector<FILE*> ref_gtf_files; + +- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames) ++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames) + { + FILE* ref_gtf = NULL; + if (ref_gtf_in_filename != "") +diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp +index 575b064..7725910 100644 +--- a/src/cuffdiff.cpp ++++ b/src/cuffdiff.cpp +@@ -490,7 +490,7 @@ void print_FPKM_tracking(FILE* fout, + const vector<FPKMContext>& fpkms = track.fpkm_series; + + AbundanceStatus status = NUMERIC_OK; +- foreach (const FPKMContext& c, fpkms) ++ for_each (const FPKMContext& c, fpkms) + { + if (c.status == NUMERIC_FAIL) + status = NUMERIC_FAIL; +@@ -811,7 +811,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + ::load_ref_rnas(mask_gtf, rt, mask_rnas, false, false); + } + +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + fac->set_ref_rnas(ref_mRNAs); + if (mask_gtf) +@@ -826,7 +826,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + int tmp_max_frag_len = 0; + + ProgressBar p_bar("Inspecting maps and determining fragment length distributions.",0); +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + #if ENABLE_THREADS + while(1) +@@ -877,7 +877,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + { + long double total_mass = 0.0; + long double total_norm_mass = 0.0; +- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups) + { + total_mass += rg->total_map_mass(); + total_norm_mass += rg->normalized_map_mass(); +@@ -886,7 +886,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + if (total_mass > 0) + { + double scaling_factor = total_mass / total_norm_mass; +- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups) + { + double scaled_mass = scaling_factor * rg->normalized_map_mass(); + +@@ -916,7 +916,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + if (most_reps != 1 && poisson_dispersion == false) + { +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + if (fac->num_replicates() == 1) + { +@@ -990,7 +990,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + shared_ptr<MassDispersionModel const> disperser; + disperser = fit_dispersion_model("pooled", scale_factors, sample_count_table); + +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + rg_props->mass_dispersion_model(disperser); + } +@@ -999,7 +999,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + long double total_norm_mass = 0.0; + long double total_mass = 0.0; +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + total_norm_mass += rg_props->normalized_map_mass(); + total_mass += rg_props->total_map_mass(); +@@ -1007,7 +1007,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + // scale the normalized masses so that both quantile total count normalization + // are roughly on the same numerical scale +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + long double new_norm = rg_props->normalized_map_mass() * (total_mass / total_norm_mass); + rg_props->normalized_map_mass(new_norm); +@@ -1039,7 +1039,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >()); + quantitate_next_locus(rt, bundle_factories, test_launcher); + bool more_loci_remain = false; +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + if (rep_fac->bundles_remain()) + { +@@ -1071,7 +1071,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + } + } + +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + rep_fac->reset(); + } +@@ -1081,9 +1081,9 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + if (corr_bias) + { + p_bar = ProgressBar("Learning bias parameters.", 0); +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { +- foreach (shared_ptr<BundleFactory> fac, rep_fac->factories()) ++ for_each (shared_ptr<BundleFactory> fac, rep_fac->factories()) + { + #if ENABLE_THREADS + while(1) +@@ -1124,7 +1124,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + boost::this_thread::sleep(boost::posix_time::milliseconds(5)); + } + #endif +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + rep_fac->reset(); + } +@@ -1167,7 +1167,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + //shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >()); + quantitate_next_locus(rt, bundle_factories, test_launcher); + bool more_loci_remain = false; +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + if (rep_fac->bundles_remain()) + { +diff --git a/src/cufflinks.cpp b/src/cufflinks.cpp +index 796af98..1030ae8 100644 +--- a/src/cufflinks.cpp ++++ b/src/cufflinks.cpp +@@ -471,7 +471,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs, + { + for(size_t l = 0; l < lhs.size(); ++l) + { +- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) + { + // if we're past all the overlaps, just stop + if (ref_scaff->left() >= lhs[l].right() + overhang_3) +@@ -504,7 +504,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs, + } + for(size_t r = 0; r < rhs.size(); ++r) + { +- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) + { + if (ref_scaff->left() >= rhs[r].right() + overhang_3) + { +@@ -665,7 +665,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle, + if (ref_guided && enable_faux_reads && !hits.empty()) + { + vector<Scaffold> pseudohits; +- foreach(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) + { + ref_scaff->tile_with_scaffs(pseudohits, tile_len, tile_off); + } +@@ -842,7 +842,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle, + } + if (assembled_successfully) + { +- foreach(Scaffold& scaff, tmp_scaffs) ++ for_each(Scaffold& scaff, tmp_scaffs) + { + scaffolds.push_back(shared_ptr<Scaffold>(new Scaffold(scaff))); + } +@@ -886,7 +886,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + + // need the avg read length for depth of coverage calculation + double avg_read_length = 0; +- foreach (MateHit& hit, hits_in_cluster) ++ for_each (MateHit& hit, hits_in_cluster) + { + if (hit.left_alignment()) + avg_read_length += hit.left_alignment()->read_len(); +@@ -905,7 +905,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + } + else + { +- foreach(shared_ptr<Abundance> ab, transfrag_cluster.abundances()) ++ for_each(shared_ptr<Abundance> ab, transfrag_cluster.abundances()) + { + ab->status(NUMERIC_HI_DATA); + } +@@ -939,7 +939,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + { + shared_ptr<Abundance> ab_i = abundances[i]; + bool found = false; +- foreach (shared_ptr<Abundance> ab_j, filtered_transcripts) ++ for_each (shared_ptr<Abundance> ab_j, filtered_transcripts) + { + if (ab_i == ab_j) + { +@@ -961,7 +961,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + transfrags_by_strand); + + +- foreach (const AbundanceGroup& strand_group, transfrags_by_strand) ++ for_each (const AbundanceGroup& strand_group, transfrags_by_strand) + { + vector<AbundanceGroup> transfrags_by_gene; + +@@ -974,7 +974,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + cluster_transcripts<ConnectByExonOverlap>(strand_group, transfrags_by_gene); + } + +- foreach(const AbundanceGroup& gene, transfrags_by_gene) ++ for_each(const AbundanceGroup& gene, transfrags_by_gene) + { + const vector<shared_ptr<Abundance> >& iso_abundances = gene.abundances(); + vector<Isoform> isoforms; +@@ -985,7 +985,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + string ref_gene_id = ""; + + double major_isoform_FPKM = 0; +- foreach (shared_ptr<Abundance> iso_ab, iso_abundances) ++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances) + { + if (iso_ab->transfrag()->is_ref()) + { +@@ -1002,7 +1002,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + major_isoform_FPKM = max(iso_ab->FPKM(), major_isoform_FPKM); + } + +- foreach (shared_ptr<Abundance> iso_ab, iso_abundances) ++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances) + { + // Calculate transcript depth of coverage and FMI from FPKM + double FPKM = iso_ab->FPKM(); +@@ -1067,7 +1067,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + { + vector<Scaffold> c; + scaffolds[i]->get_complete_subscaffolds(c); +- foreach (Scaffold& s, c) ++ for_each (Scaffold& s, c) + { + split_partials.push_back(shared_ptr<Scaffold>(new Scaffold(s))); + } +@@ -1076,7 +1076,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + scaffolds = split_partials; + + vector<shared_ptr<Abundance> > abundances; +- foreach(shared_ptr<Scaffold> s, scaffolds) ++ for_each(shared_ptr<Scaffold> s, scaffolds) + { + TranscriptAbundance* pT = new TranscriptAbundance; + pT->transfrag(s); +@@ -1091,7 +1091,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + cluster_transcripts<ConnectByExonOverlap>(transfrags, + transfrags_by_cluster); + +- foreach(AbundanceGroup& cluster, transfrags_by_cluster) ++ for_each(AbundanceGroup& cluster, transfrags_by_cluster) + { + quantitate_transcript_cluster(cluster, total_map_mass, genes, bundle_too_large); + } +@@ -1233,10 +1233,10 @@ void assemble_bundle(const RefSequenceTable& rt, + if (init_bundle_mode == REF_GUIDED) + { + hit_introns = new set<AugmentedCuffOp>(); +- foreach(const MateHit& h, bundle.non_redundant_hits()) ++ for_each(const MateHit& h, bundle.non_redundant_hits()) + { + Scaffold s(h); +- foreach (AugmentedCuffOp a, s.augmented_ops()) ++ for_each (AugmentedCuffOp a, s.augmented_ops()) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1567,7 +1567,7 @@ void driver(const string& hit_file_name, FILE* ref_gtf, FILE* mask_gtf) + verbose_msg("%d ReadHits still live\n", num_deleted); + verbose_msg("Found %lu reference contigs\n", rt.size()); + +- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) ++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) + { + ref_scaff->clear_hits(); + } +diff --git a/src/differential.cpp b/src/differential.cpp +index 3e5cff0..6b108cb 100644 +--- a/src/differential.cpp ++++ b/src/differential.cpp +@@ -84,7 +84,7 @@ void TestLauncher::abundance_avail(const string& locus_id, + // acquire the lock itself. + bool TestLauncher::all_samples_reported_in(vector<shared_ptr<SampleAbundances> >& abundances) + { +- foreach (shared_ptr<SampleAbundances> ab, abundances) ++ for_each (shared_ptr<SampleAbundances> ab, abundances) + { + if (!ab) + { +@@ -436,7 +436,7 @@ pair<int, SampleDiffs::iterator> get_de_tests(const string& description, + // ublas::vector<double> null_kappa_mean; + // null_kappa_mean = ublas::zero_vector<double>(curr_kappa_cov.size1()); + // +-// foreach(ublas::vector<double>& sample, samples) ++// for_each(ublas::vector<double>& sample, samples) + // { + // null_kappa_mean += sample; + // } +@@ -1056,7 +1056,7 @@ void sample_abundance_worker(const string& locus_tag, + { + vector<shared_ptr<Abundance> > abundances; + +- foreach(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds()) + { + TranscriptAbundance* pT = new TranscriptAbundance; + pT->transfrag(s); +@@ -1082,7 +1082,7 @@ void sample_abundance_worker(const string& locus_tag, + } + else + { +- foreach(shared_ptr<Abundance> ab, abundances) ++ for_each(shared_ptr<Abundance> ab, abundances) + { + ab->status(NUMERIC_HI_DATA); + } +@@ -1093,7 +1093,7 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(sample.transcripts, + transcripts_by_gene_id); + +- foreach(AbundanceGroup& ab_group, transcripts_by_gene_id) ++ for_each(AbundanceGroup& ab_group, transcripts_by_gene_id) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); +@@ -1119,7 +1119,7 @@ void sample_abundance_worker(const string& locus_tag, + &cds_count_cov, + &cds_fpkm_cov, + &cds_gamma_boot_cov); +- foreach(AbundanceGroup& ab_group, transcripts_by_cds) ++ for_each(AbundanceGroup& ab_group, transcripts_by_cds) + { + ab_group.locus_tag(locus_tag); + set<string> protein_ids = ab_group.protein_id(); +@@ -1135,7 +1135,7 @@ void sample_abundance_worker(const string& locus_tag, + vector<shared_ptr<Abundance> > cds_abundances; + double max_cds_mass_variance = 0.0; + set<shared_ptr<ReadGroupProperties const> > rg_props; +- foreach (AbundanceGroup& ab_group, sample.cds) ++ for_each (AbundanceGroup& ab_group, sample.cds) + { + cds_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group))); + max_cds_mass_variance = max(ab_group.max_mass_variance(), max_cds_mass_variance); +@@ -1155,7 +1155,7 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(cds, + cds_by_gene); + +- foreach(AbundanceGroup& ab_group, cds_by_gene) ++ for_each(AbundanceGroup& ab_group, cds_by_gene) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); +@@ -1185,7 +1185,7 @@ void sample_abundance_worker(const string& locus_tag, + &tss_gamma_boot_cov); + + +- foreach(AbundanceGroup& ab_group, transcripts_by_tss) ++ for_each(AbundanceGroup& ab_group, transcripts_by_tss) + { + ab_group.locus_tag(locus_tag); + set<string> tss_ids = ab_group.tss_id(); +@@ -1202,7 +1202,7 @@ void sample_abundance_worker(const string& locus_tag, + // Group TSS clusters by gene + vector<shared_ptr<Abundance> > primary_transcript_abundances; + set<shared_ptr<ReadGroupProperties const> > rg_props; +- foreach (AbundanceGroup& ab_group, sample.primary_transcripts) ++ for_each (AbundanceGroup& ab_group, sample.primary_transcripts) + { + primary_transcript_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group))); + max_tss_mass_variance = max(max_tss_mass_variance, ab_group.max_mass_variance()); +@@ -1223,13 +1223,13 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(primary_transcripts, + primary_transcripts_by_gene); + +- foreach(AbundanceGroup& ab_group, primary_transcripts_by_gene) ++ for_each(AbundanceGroup& ab_group, primary_transcripts_by_gene) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); + // if (gene_ids.size() > 1) + // { +-// foreach (string st, gene_ids) ++// for_each (string st, gene_ids) + // { + // fprintf(stderr, "%s\n", st.c_str()); + // } +@@ -1314,7 +1314,7 @@ void sample_worker(const RefSequenceTable& rt, + bool perform_cds_analysis = final_est_run; + bool perform_tss_analysis = final_est_run; + +- foreach(shared_ptr<Scaffold> s, bundle.ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> s, bundle.ref_scaffolds()) + { + if (s->annotated_tss_id() == "") + { +@@ -1439,7 +1439,7 @@ void sample_worker(const RefSequenceTable& rt, + /////////////////////////////////////////////// + + +- foreach(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds()) + { + ref_scaff->clear_hits(); + } +@@ -1465,7 +1465,7 @@ void dump_locus_variance_info(const string& filename) + + fprintf(fdump, + "condition\tdescription\tlocus_counts\tempir_var\tlocus_fit_var\tsum_iso_fit_var\tcross_replicate_js\tnum_transcripts\tbayes_gamma_trace\tempir_gamma_trace\tcount_mean\tgamma_var\tgamma_bootstrap_var\tlocus_salient_frags\tlocus_total_frags\tcount_sharing\n"); +- foreach (LocusVarianceInfo& L, locus_variance_info_table) ++ for_each (LocusVarianceInfo& L, locus_variance_info_table) + { + for (size_t i = 0; i < L.gamma.size(); ++i) + { +@@ -1503,22 +1503,22 @@ void test_differential(const string& locus_tag, + for (size_t i = 0; i < samples.size(); ++i) + { + const AbundanceGroup& ab_group = samples[i]->transcripts; +- foreach (shared_ptr<Abundance> ab, ab_group.abundances()) ++ for_each (shared_ptr<Abundance> ab, ab_group.abundances()) + { + add_to_tracking_table(i, *ab, tracking.isoform_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->cds) ++ for_each (AbundanceGroup& ab, samples[i]->cds) + { + add_to_tracking_table(i, ab, tracking.cds_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->primary_transcripts) ++ for_each (AbundanceGroup& ab, samples[i]->primary_transcripts) + { + add_to_tracking_table(i, ab, tracking.tss_group_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->genes) ++ for_each (AbundanceGroup& ab, samples[i]->genes) + { + add_to_tracking_table(i, ab, tracking.gene_fpkm_tracking); + } +diff --git a/src/filters.cpp b/src/filters.cpp +index 0a10b50..5ab31e0 100644 +--- a/src/filters.cpp ++++ b/src/filters.cpp +@@ -752,7 +752,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + + if (library_type != "transfrags") + { +- foreach (Scaffold& scaff, scaffolds) ++ for_each (Scaffold& scaff, scaffolds) + { + if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV)) + continue; +@@ -761,7 +761,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + vector<double> coverage(scaff_len, 0.0); + + double total = 0; +- foreach(const MateHit* hit, scaff.mate_hits()) ++ for_each(const MateHit* hit, scaff.mate_hits()) + { + int start, end, frag_len; + if (!scaff.map_frag(*hit, start, end, frag_len)) continue; +@@ -906,7 +906,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + } + else + { +- foreach (Scaffold& scaff, scaffolds) ++ for_each (Scaffold& scaff, scaffolds) + { + if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV)) + continue; +@@ -915,7 +915,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + vector<double> coverage(scaff_len, 0.0); + + double total = 0; +- foreach(const MateHit* hit, scaff.mate_hits()) ++ for_each(const MateHit* hit, scaff.mate_hits()) + { + int start, end, frag_len; + if (!scaff.map_frag(*hit, start, end, frag_len)) continue; +diff --git a/src/genes.h b/src/genes.h +index 4dfa996..eb48a14 100644 +--- a/src/genes.h ++++ b/src/genes.h +@@ -169,7 +169,7 @@ public: + + bool has_ref_trans() const + { +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + if (iso.is_ref_trans()) + return true; +@@ -180,7 +180,7 @@ public: + double estimated_count() const + { + double est = 0.0; +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + est += iso.estimated_count(); + } +@@ -191,7 +191,7 @@ public: + { + double eff = 0.0; + double total_fpkm = 0; +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + eff += iso.FPKM() * iso.effective_length(); + total_fpkm += iso.FPKM(); +diff --git a/src/gtf_to_sam.cpp b/src/gtf_to_sam.cpp +index 12f70c1..f52d40a 100644 +--- a/src/gtf_to_sam.cpp ++++ b/src/gtf_to_sam.cpp +@@ -241,13 +241,13 @@ void set_relative_fpkms(vector<shared_ptr<Scaffold> >& ref_mRNAs) + vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i]; + + double total_fpkm = 0.0; +- foreach(shared_ptr<Scaffold> scaff, gene) ++ for_each(shared_ptr<Scaffold> scaff, gene) + { + total_fpkm += scaff->fpkm(); + } + if (total_fpkm > 0) + { +- foreach (shared_ptr<Scaffold> scaff, gene) ++ for_each (shared_ptr<Scaffold> scaff, gene) + { + scaff->fpkm(scaff->fpkm() / total_fpkm); + } +@@ -263,7 +263,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* sam_out) + vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table; + vector<pair<string, vector<double> > > sample_count_table; + +- foreach (FILE* ref_gtf, ref_gtf_files) ++ for_each (FILE* ref_gtf, ref_gtf_files) + { + vector<shared_ptr<Scaffold> > ref_mRNAs; + ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true); +@@ -314,7 +314,7 @@ int main(int argc, char** argv) + + vector<FILE*> ref_gtf_files; + +- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames) ++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames) + { + FILE* ref_gtf = NULL; + if (ref_gtf_in_filename != "") +diff --git a/src/hits.cpp b/src/hits.cpp +index 910ba0f..dc81813 100644 +--- a/src/hits.cpp ++++ b/src/hits.cpp +@@ -233,7 +233,7 @@ void collapse_hits(const vector<MateHit>& hits, + non_redundant.erase(new_end, non_redundant.end()); + non_redundant.resize(non_redundant.size()); + +- foreach(MateHit& hit, non_redundant) ++ for_each(MateHit& hit, non_redundant) + hit.collapse_mass(0); + + size_t curr_aln = 0; +@@ -252,7 +252,7 @@ void collapse_hits(const vector<MateHit>& hits, + ++curr_aln; + } + +- //foreach(MateHit& hit, non_redundant) ++ //for_each(MateHit& hit, non_redundant) + //assert(hit.collapse_mass() <= 1 || !hit.is_multi()); + + //non_redundant.erase(remove_if(non_redundant.begin(),non_redundant.end(),has_no_collapse_mass), non_redundant.end()); +diff --git a/src/replicates.cpp b/src/replicates.cpp +index 634f209..ec8ce9c 100644 +--- a/src/replicates.cpp ++++ b/src/replicates.cpp +@@ -236,7 +236,7 @@ fit_dispersion_model_helper(const string& condition_name, + mean /= p.counts.size(); + + double var = 0.0; +- foreach (double d, p.counts) ++ for_each (double d, p.counts) + { + var += (d - mean) * (d - mean); + } +@@ -363,7 +363,7 @@ fit_dispersion_model(const string& condition_name, + ProgressBar p_bar("Modeling fragment count overdispersion.",0); + + int max_transcripts = 0; +- foreach(const LocusCountList& L, sample_count_table) ++ for_each(const LocusCountList& L, sample_count_table) + { + if (L.num_transcripts > max_transcripts) + { +@@ -382,7 +382,7 @@ fit_dispersion_model(const string& condition_name, + if (i != 0) + { + // vector<LocusCountList> sample_count_subtable; +-// foreach(const LocusCountList& L, sample_count_table) ++// for_each(const LocusCountList& L, sample_count_table) + // { + // if (L.num_transcripts == i) + // { +diff --git a/src/replicates.h b/src/replicates.h +index ca4484f..73d339c 100644 +--- a/src/replicates.h ++++ b/src/replicates.h +@@ -99,7 +99,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach (boost::shared_ptr<BundleFactory> fac, _factories) ++ for_each (boost::shared_ptr<BundleFactory> fac, _factories) + { + if (fac->bundles_remain()) + return true; +@@ -115,7 +115,7 @@ public: + std::vector<HitBundle*> bundles; + + bool non_empty_bundle = false; +- foreach (boost::shared_ptr<BundleFactory> fac, _factories) ++ for_each (boost::shared_ptr<BundleFactory> fac, _factories) + { + bundles.push_back(new HitBundle()); + if (fac->next_bundle(*(bundles.back()))) +@@ -126,7 +126,7 @@ public: + + if (non_empty_bundle == false) + { +- foreach (HitBundle* in_bundle, bundles) ++ for_each (HitBundle* in_bundle, bundles) + { + in_bundle->ref_scaffolds().clear(); + in_bundle->clear_hits(); +@@ -149,7 +149,7 @@ public: + // Merge the replicates into a combined bundle of hits. + HitBundle::combine(bundles, bundle_out); + +- foreach (HitBundle* in_bundle, bundles) ++ for_each (HitBundle* in_bundle, bundles) + { + in_bundle->ref_scaffolds().clear(); + in_bundle->clear_hits(); +@@ -163,7 +163,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach (shared_ptr<BundleFactory> fac, _factories) ++ for_each (shared_ptr<BundleFactory> fac, _factories) + { + fac->reset(); + } +@@ -246,7 +246,7 @@ public: + shared_ptr<MassDispersionModel const> disperser; + disperser = fit_dispersion_model(_condition_name,scale_factors, sample_count_table); + +- foreach (shared_ptr<BundleFactory> fac, _factories) ++ for_each (shared_ptr<BundleFactory> fac, _factories) + { + shared_ptr<ReadGroupProperties> rg_props = fac->read_group_properties(); + rg_props->mass_dispersion_model(disperser); +@@ -260,7 +260,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory> fac, _factories) ++ for_each(shared_ptr<BundleFactory> fac, _factories) + { + fac->set_ref_rnas(mRNAs); + } +@@ -271,7 +271,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory> fac, _factories) ++ for_each(shared_ptr<BundleFactory> fac, _factories) + { + fac->set_mask_rnas(mRNAs); + } +@@ -284,7 +284,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory>& fac, _factories) ++ for_each(shared_ptr<BundleFactory>& fac, _factories) + { + fac->read_group_properties()->mass_dispersion_model(disperser); + } +diff --git a/src/scaffolds.cpp b/src/scaffolds.cpp +index 096f58a..c12118e 100644 +--- a/src/scaffolds.cpp ++++ b/src/scaffolds.cpp +@@ -620,7 +620,7 @@ void Scaffold::tile_with_scaffs(vector<Scaffold>& tile_scaffs, int max_len, int + + // genomic_offset actually could be zero - from an exon starting at coord + // 1 in some chromosome of the ref. +-// foreach(const AugmentedCuffOp& op, ops) ++// for_each(const AugmentedCuffOp& op, ops) + // { + // assert (op.genomic_offset != 0); + // } +@@ -819,7 +819,7 @@ void Scaffold::merge(const vector<Scaffold>& s, + if (library_type == "transfrags") + { + double avg_fpkm = 0.0; +- foreach (const Scaffold& sc, s) ++ for_each (const Scaffold& sc, s) + { + avg_fpkm += sc.fpkm(); + } +@@ -871,7 +871,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler) + + vector<AugmentedCuffOp> tmp_filler = filler; + +- foreach(const AugmentedCuffOp& op, orig_ops) ++ for_each(const AugmentedCuffOp& op, orig_ops) + { + assert (op.g_left() < op.g_right()); + +@@ -888,7 +888,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler) + AugmentedCuffOp::merge_ops(tmp_filler, padded_filler, false); + + vector<AugmentedCuffOp> overlapping; +- foreach (const AugmentedCuffOp& op, padded_filler) ++ for_each (const AugmentedCuffOp& op, padded_filler) + { + //if (left() <= op.g_left() && right() >= op.g_right() + if(::overlap_in_genome(op.g_left(),op.g_right(), left(), right()) +@@ -1630,7 +1630,7 @@ void Scaffold::get_complete_subscaffolds(vector<Scaffold>& complete) + + // const vector<const MateHit*>& hits = known.mate_hits(); + // bool contains_spliced_hit = false; +- // foreach (const MateHit* h, hits) ++ // for_each (const MateHit* h, hits) + // { + // const ReadHit* left = h->left_alignment(); + // const ReadHit* right = h->right_alignment(); +@@ -1670,7 +1670,7 @@ double Scaffold::internal_exon_coverage() const + int left = augmented_ops()[2].g_left(); + int right = augmented_ops()[augmented_ops().size() - 3].g_right(); + vector<bool> covered(right-left, 0); +- foreach(const MateHit* h, mate_hits()) ++ for_each(const MateHit* h, mate_hits()) + { + if (::overlap_in_genome(h->left(),h->right(), left, right)) + { +@@ -1694,7 +1694,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con + if (has_intron()) + return true; + +- foreach (const MateHit* h, mate_hits()) ++ for_each (const MateHit* h, mate_hits()) + { + if (h->strand() == strand()) + return true; +@@ -1704,7 +1704,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con + if (ref_scaffs == NULL) + return false; + +- foreach (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) ++ for_each (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) + { + if (ref_scaff->strand() == strand() && exons_overlap(*this, *ref_scaff)) + return true; +@@ -1729,10 +1729,10 @@ bool Scaffold::hits_support_introns() const + { + set<AugmentedCuffOp> hit_introns; + set<AugmentedCuffOp> scaffold_introns; +- foreach(const MateHit* h, _mates_in_scaff) ++ for_each(const MateHit* h, _mates_in_scaff) + { + Scaffold s(*h); +- foreach (AugmentedCuffOp a, s.augmented_ops()) ++ for_each (AugmentedCuffOp a, s.augmented_ops()) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1740,7 +1740,7 @@ bool Scaffold::hits_support_introns() const + } + } + } +- foreach (AugmentedCuffOp a, _augmented_ops) ++ for_each (AugmentedCuffOp a, _augmented_ops) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1751,13 +1751,13 @@ bool Scaffold::hits_support_introns() const + if (hit_introns != scaffold_introns) + { + fprintf(stderr, "********************\n"); +- foreach(const AugmentedCuffOp& a, hit_introns) ++ for_each(const AugmentedCuffOp& a, hit_introns) + { + fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right()); + } + + fprintf(stderr, "####################\n"); +- foreach(const AugmentedCuffOp& a, scaffold_introns) ++ for_each(const AugmentedCuffOp& a, scaffold_introns) + { + fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right()); + } +@@ -1770,7 +1770,7 @@ bool Scaffold::hits_support_introns(set<AugmentedCuffOp>& hit_introns) const + { + set<AugmentedCuffOp> scaffold_introns; + +- foreach (AugmentedCuffOp a, _augmented_ops) ++ for_each (AugmentedCuffOp a, _augmented_ops) + { + if (a.opcode == CUFF_INTRON) + { +diff --git a/src/scaffolds.h b/src/scaffolds.h +index 0f29e80..f8410f7 100644 +--- a/src/scaffolds.h ++++ b/src/scaffolds.h +@@ -314,7 +314,7 @@ public: + if (library_type == "transfrags") + { + double avg_fpkm = 0.0; +- foreach (const Scaffold& sc, hits) ++ for_each (const Scaffold& sc, hits) + { + avg_fpkm += sc.fpkm(); + } diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch new file mode 100644 index 000000000000..360e9c1a11b8 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch @@ -0,0 +1,20 @@ + src/lemon/bits/base_extender.h | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/lemon/bits/base_extender.h b/src/lemon/bits/base_extender.h +index 84bb242..b812247 100644 +--- a/src/lemon/bits/base_extender.h ++++ b/src/lemon/bits/base_extender.h +@@ -359,10 +359,10 @@ namespace lemon { + } + + Node source(const UEdge& edge) const { +- return aNode(edge); ++ return this->aNode(edge); + } + Node target(const UEdge& edge) const { +- return bNode(edge); ++ return this->bNode(edge); + } + + void firstInc(UEdge& edge, bool& dir, const Node& node) const { diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch new file mode 100644 index 000000000000..47784088fab9 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch @@ -0,0 +1,28 @@ + configure.ac | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 96ffbac..e88b8e4 100755 +--- a/configure.ac ++++ b/configure.ac +@@ -61,7 +61,8 @@ AC_CANONICAL_HOST + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" ++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" ++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" + ext_CFLAGS="" + debug_CFLAGS="" + #echo "${host_cpu}-${host_os}" +@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS" +-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" ++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" ++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" + user_LDFLAGS="$LDFLAGS" + LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch new file mode 100644 index 000000000000..3b9abd812680 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch @@ -0,0 +1,16 @@ + ax_bam.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ax_bam.m4 b/ax_bam.m4 +index 7d463b7..95f1bed 100644 +--- a/ax_bam.m4 ++++ b/ax_bam.m4 +@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then + AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) + fi + else +- BAM_LIB="-lbam" ++ BAM_LIB="-lbam -lhts" + AC_SUBST(BAM_CPPFLAGS) + AC_SUBST(BAM_LDFLAGS) + AC_SUBST(BAM_LIB) diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/cufflinks/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/cutg/Manifest b/sci-biology/cutg/Manifest new file mode 100644 index 000000000000..5c0e901d9aba --- /dev/null +++ b/sci-biology/cutg/Manifest @@ -0,0 +1 @@ +DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93 diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild new file mode 100644 index 000000000000..46163bc2a80f --- /dev/null +++ b/sci-biology/cutg/cutg-160-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Codon usage tables calculated from GenBank" +HOMEPAGE="http://www.kazusa.or.jp/codon/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + mkdir CODONS || die + ebegin "Indexing CUTG for usage with EMBOSS." + EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \ + "Indexing CUTG failed." + eend + fi +} + +src_install() { + local file + dodoc README CODON_LABEL SPSUM_LABEL + if ! use minimal; then + dodir /usr/share/${PN} + mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ + "Installing raw CUTG database failed." + fi + + if use emboss; then + dodir /usr/share/EMBOSS/data/CODONS + cd CODONS || die + for file in *; do + mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \ + "Installing the EMBOSS-indexed database failed." + done + fi +} diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml new file mode 100644 index 000000000000..59b110912ca6 --- /dev/null +++ b/sci-biology/cutg/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-biology</herd> + <longdescription> + Codon usage tables maintained at the Kazusa DNA Research Institute. + Codon usage in individual genes has been calculated using the + nucleotide sequence data obtained from the GenBank Genetic Sequence + Database. The compilation of codon usage is synchronized with each + major release of GenBank. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest new file mode 100644 index 000000000000..de90a59afc93 --- /dev/null +++ b/sci-biology/dialign-tx/Manifest @@ -0,0 +1 @@ +DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild new file mode 100644 index 000000000000..c73d043742b8 --- /dev/null +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +MY_P=DIALIGN-TX_${PV} + +DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-tx.gobics.de/" +SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \ + -i source/Makefile || die #336533 + epatch "${FILESDIR}"/${P}-implicits.patch +} + +src_compile() { + emake -C source clean + emake -C source CC="$(tc-getCC)" \ + CPPFLAGS="" +} + +src_install() { + dobin "${S}"/source/dialign-tx + insinto /usr/$(get_libdir)/${PN}/conf + doins "${S}"/conf/* +} + +pkg_postinst() { + einfo "The configuration directory is" + einfo "${ROOT}usr/$(get_libdir)/${PN}/conf" + einfo "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch new file mode 100644 index 000000000000..a8388d03232f --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -0,0 +1,18 @@ +--- source/museq.c ++++ source/museq.c +@@ -38,6 +38,7 @@ + //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + // struct prob_dist *pdist); + //extern struct diag_col *create_diag_col(int seq_amount); ++extern void free_diag(struct diag* dg); + extern void free_diag_col(struct diag_col* dcol); + extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, + struct prob_dist *pdist, +@@ -52,6 +53,7 @@ + + // alig.c + extern struct alignment* create_empty_alignment(struct seq_col *scol); ++extern void free_alignment(struct alignment *algn); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, + struct scr_matrix* smatrix, diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/dialign-tx/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/dialign2/Manifest b/sci-biology/dialign2/Manifest new file mode 100644 index 000000000000..8f3f4080e56f --- /dev/null +++ b/sci-biology/dialign2/Manifest @@ -0,0 +1 @@ +DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84 diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1.ebuild new file mode 100644 index 000000000000..58557729b529 --- /dev/null +++ b/sci-biology/dialign2/dialign2-2.2.1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Multiple sequence alignment" +HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" +SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/dialign_package + +src_compile() { + emake -C src \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -I. -DCONS -c" +} + +src_install() { + dobin src/${PN}-2 + insinto /usr/share/${PN} + doins dialign2_dir/* + + cat >> "${T}"/80${PN} <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/80${PN} +} diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml new file mode 100644 index 000000000000..7bc6ee8ea837 --- /dev/null +++ b/sci-biology/dialign2/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest new file mode 100644 index 000000000000..fe0ae5f610cb --- /dev/null +++ b/sci-biology/diya/Manifest @@ -0,0 +1 @@ +DIST diya-1.0-rc4.tar.gz 386706 SHA256 13f7dd4dd7f96143948587884954e337552d7491347c2c174e786824880590c7 diff --git a/sci-biology/diya/diya-1.0_rc4.ebuild b/sci-biology/diya/diya-1.0_rc4.ebuild new file mode 100644 index 000000000000..2211525f8af9 --- /dev/null +++ b/sci-biology/diya/diya-1.0_rc4.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module + +DESCRIPTION="Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation" +HOMEPAGE="http://gmod.org/wiki/Diya" +SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="-minimal" +KEYWORDS="~amd64 ~x86" + +DEPEND="sci-biology/bioperl + dev-perl/Data-Utilities + dev-perl/XML-Simple" +RDEPEND="${DEPEND} + !minimal? ( + sci-biology/mummer + sci-biology/glimmer + sci-biology/trnascan-se + sci-biology/infernal )" + +# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++ +# * rfamscan.pl v0.1 (http://www.sanger.ac.uk/Users/sgj/code/) +# * UniRef50 (http://www.ebi.ac.uk/uniref/) +# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/) +# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/. + +S="${WORKDIR}/diya-${PV/_/-}" + +SRC_TEST=do + +src_install() { + mydoc="INSTALL README docs/diya.html" + perl-module_src_install + insinto /usr/share/${PN} + doins -r diya.conf docs examples scripts +} diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml new file mode 100644 index 000000000000..d6b9de8b20a7 --- /dev/null +++ b/sci-biology/diya/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-biology</herd> + <upstream> + <remote-id type="sourceforge">diyg</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest new file mode 100644 index 000000000000..60015030796d --- /dev/null +++ b/sci-biology/elph/Manifest @@ -0,0 +1,2 @@ +DIST ELPH-0.1.5.tar.gz 153150 RMD160 7e60e2cf9a99cb435768cebbcd1506164e8a901c SHA1 1a3820c851ac0d021c9696ba1fd4eec819d82dbc SHA256 6ffa160f85cb2569bdf869cb0514dc624afcef4f2d8a36efbd1228d1a16cf361 +DIST ELPH-1.0.1.tar.gz 113476 RMD160 854bc34aba30f1c7493536e1b2e36dd8143af7e7 SHA1 9c8bf6ac54ade29daa15dc07aeeb94747626298a SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild new file mode 100644 index 000000000000..5fc361ace8fd --- /dev/null +++ b/sci-biology/elph/elph-0.1.5.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +LICENSE="Artistic" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="x86" + +S="${WORKDIR}/ELPH/sources" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-usage.patch + sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" \ + -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" \ + -e "s/LINKER := g++/LINKER := $(tc-getCXX)/" \ + Makefile || die "Failed to patch Makefile." +} + +src_compile() { + make || die "Compilation failed." +} + +src_install() { + dobin elph || die "Failed to install program." + cd "${WORKDIR}"/ELPH + dodoc VERSION || die "Documentation installation failed." + newdoc Readme.ELPH README || die "Readme installation failed." +} diff --git a/sci-biology/elph/elph-1.0.1.ebuild b/sci-biology/elph/elph-1.0.1.ebuild new file mode 100644 index 000000000000..78476added83 --- /dev/null +++ b/sci-biology/elph/elph-1.0.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +LICENSE="Artistic" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +S=${WORKDIR}/ELPH/sources + +src_compile() { + emake CC="$(tc-getCXX)" LINKER="$(tc-getCXX)" \ + CFLAGS="${CXXFLAGS} -D_REENTRANT" LDFLAGS="${LDFLAGS}" || die +} + +src_install() { + dobin elph || die "Failed to install program." + cd "${WORKDIR}"/ELPH + dodoc VERSION || die "Documentation installation failed." + newdoc Readme.ELPH README || die "Readme installation failed." +} diff --git a/sci-biology/elph/files/elph-0.1.4-usage.patch b/sci-biology/elph/files/elph-0.1.4-usage.patch new file mode 100644 index 000000000000..be49e2d1ebb8 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.4-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc~ 2003-06-03 14:45:22.000000000 -0400 ++++ elph.cc 2004-10-30 10:14:49.220415168 -0400 +@@ -26,11 +26,11 @@ + period variable\n\ + -x : print maximum positions within sequences\n\ + -g : find significance of motif\n\ +- -t <matrix> : test if there is significant difference between the two +- input files for a given motif matrix; <matrix> is the file ++ -t <matrix> : test if there is significant difference between the two\n\ ++ input files for a given motif matrix; <matrix> is the file\n\ + containing the motif matrix\n\ +- -l : compute Least Likely Consensus (LLC) for given motif +- -c : in conjunction with -m option: motif is not necessarily in ++ -l : compute Least Likely Consensus (LLC) for given motif\n\ ++ -c : in conjunction with -m option: motif is not necessarily in\n\ + the closest edit distance from input motif\n\ + LEN=n : n = length of motif\n\ + ITERNO=n : n = no of iterations to compute the global maximum;\n\ +@@ -41,7 +41,7 @@ + default = 1000\n\ + " + +-// global variables: ++// global variables: + int ITER_NO=10; + int MAX_LOOP=500; + int printmax=0; +@@ -66,7 +66,7 @@ + seqType t; + + GArgs args(argc, argv, "ho:abglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); +- ++ + // == Process arguments. + + int e; +@@ -83,7 +83,7 @@ + + if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files + +- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); ++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); + M->twofilesignif(gdet,testfile,SignifNo,print,pattern); + + } +@@ -93,11 +93,11 @@ + // given motif + + M = new Motif(infile,outf,t,pattern); +- if(defLLC) { ++ if(defLLC) { + double llc=M->computeLLC(pattern,print); + fprintf(outf,"LLC = %f\n",llc); + } +- ++ + } + else { + +@@ -108,7 +108,7 @@ + } + + double globAlignProb; +- ++ + globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); + + +@@ -116,13 +116,13 @@ + /*info=M->InfoPar(globAlignProb); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); + M->printMotif();*/ +- ++ + // optimizing + fprintf(stderr,"Optimizing...\n"); + globAlignProb=M->optimize(globAlignProb,info,closest); + fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); +- ++ + if(runsignif) { + M->runforsignif(SignifNo,print,gdet,pattern); + } +@@ -134,17 +134,17 @@ + + seqType Process_Options(GArgs* args) + { +- +- if (args->startNonOpt()) { //parse the non-options arguments ++ ++ if (args->startNonOpt()) { //parse the non-options arguments + //(usually filenames) + infile=args->nextNonOpt(); + } + +- if (infile.is_empty() || args->getOpt('h')!=NULL) ++ if (infile.is_empty() || args->getOpt('h')!=NULL) + GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input + + testfile=args->nextNonOpt(); +- ++ + GString outfile=args->getOpt('o'); + if (!outfile.is_empty()) { + outf=fopen(outfile, "w"); +@@ -156,7 +156,7 @@ + matrixfile=args->getOpt('t'); + + GString param; +- ++ + pattern=args->getOpt('m'); + if(pattern.is_empty()) { + param=args->getOpt("LEN"); +@@ -200,7 +200,7 @@ + + seqType t; + if(args->getOpt('a')!=NULL) t=aac; else t=nucl; +- ++ + return(t); + + } +@@ -210,7 +210,7 @@ + Motif *M; + + double llcmax=-HUGE_VAL; +- GString seed; ++ GString seed; + for(int i1=0;i1<4;i1++) + for(int i2=0;i2<4;i2++) + for(int i3=0;i3<4;i3++) diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch new file mode 100644 index 000000000000..139b83c1c1c6 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.5-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc.old 2005-01-11 14:17:47.000000000 -0500 ++++ elph.cc 2005-01-27 19:42:30.218350552 -0500 +@@ -26,11 +26,11 @@ + period variable\n\ + -x : print maximum positions within sequences\n\ + -g : find significance of motif\n\ +- -t <matrix> : test if there is significant difference between the two +- input files for a given motif matrix; <matrix> is the file ++ -t <matrix> : test if there is significant difference between the two\n\ ++ input files for a given motif matrix; <matrix> is the file\n\ + containing the motif matrix\n\ +- -l : compute Least Likely Consensus (LLC) for given motif +- -c : in conjunction with -m option: motif is not necessarily in ++ -l : compute Least Likely Consensus (LLC) for given motif\n\ ++ -c : in conjunction with -m option: motif is not necessarily in\n\ + the closest edit distance from input motif\n\ + LEN=n : n = length of motif\n\ + ITERNO=n : n = no of iterations to compute the global maximum;\n\ +@@ -41,7 +41,7 @@ + default = 1000\n\ + " + +-// global variables: ++// global variables: + int ITER_NO=10; + int MAX_LOOP=500; + int printmax=0; +@@ -66,7 +66,7 @@ + seqType t; + + GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); +- ++ + // == Process arguments. + + int e; +@@ -83,7 +83,7 @@ + + if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files + +- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); ++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); + M->twofilesignif(gdet,testfile,SignifNo,print,pattern); + + } +@@ -93,11 +93,11 @@ + // given motif + + M = new Motif(infile,outf,t,pattern); +- if(defLLC) { ++ if(defLLC) { + double llc=M->computeLLC(pattern,print); + fprintf(outf,"LLC = %f\n",llc); + } +- ++ + } + else { + +@@ -108,7 +108,7 @@ + } + + double globAlignProb; +- ++ + globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); + + +@@ -116,13 +116,13 @@ + /*info=M->InfoPar(globAlignProb); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); + M->printMotif();*/ +- ++ + // optimizing + fprintf(stderr,"Optimizing...\n"); + globAlignProb=M->optimize(globAlignProb,info,closest); + fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); +- ++ + if(runsignif) { + M->runforsignif(SignifNo,print,gdet,pattern); + } +@@ -134,17 +134,17 @@ + + seqType Process_Options(GArgs* args) + { +- +- if (args->startNonOpt()) { //parse the non-options arguments ++ ++ if (args->startNonOpt()) { //parse the non-options arguments + //(usually filenames) + infile=args->nextNonOpt(); + } + +- if (infile.is_empty() || args->getOpt('h')!=NULL) ++ if (infile.is_empty() || args->getOpt('h')!=NULL) + GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input + + testfile=args->nextNonOpt(); +- ++ + GString outfile=args->getOpt('o'); + if (!outfile.is_empty()) { + outf=fopen(outfile, "w"); +@@ -156,7 +156,7 @@ + matrixfile=args->getOpt('t'); + + GString param; +- ++ + pattern=args->getOpt('m'); + if(pattern.is_empty()) { + param=args->getOpt("LEN"); +@@ -200,7 +200,7 @@ + + seqType t; + if(args->getOpt('a')!=NULL) t=aac; else t=nucl; +- ++ + return(t); + + } +@@ -210,7 +210,7 @@ + Motif *M; + + double llcmax=-HUGE_VAL; +- GString seed; ++ GString seed; + for(int i1=0;i1<4;i1++) + for(int i2=0;i2<4;i2++) + for(int i3=0;i3<4;i3++) diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml new file mode 100644 index 000000000000..469879ba8f5b --- /dev/null +++ b/sci-biology/elph/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-biology</herd> + <longdescription> + ELPH is a general-purpose Gibbs sampler for finding motifs in a set of + DNA or protein sequences. The program takes as input a set containing + anywhere from a few dozen to thousands of sequences, and searches + through them for the most common motif, assuming that each sequence + contains one copy of the motif. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest new file mode 100644 index 000000000000..408037d6a1ec --- /dev/null +++ b/sci-biology/embassy-cbstools/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693 +DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild new file mode 100644 index 000000000000..b2f9738aa495 --- /dev/null +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Applications from the CBS group" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild new file mode 100644 index 000000000000..ca1539905c99 --- /dev/null +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for applications from the CBS group" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..d29310efcb47 --- /dev/null +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index a70d4d2..b8f5e79 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 824a03c..9db171d 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-cbstools/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/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest new file mode 100644 index 000000000000..43c85d868e12 --- /dev/null +++ b/sci-biology/embassy-clustalomega/Manifest @@ -0,0 +1 @@ +DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54 diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild new file mode 100644 index 000000000000..620383da2eb0 --- /dev/null +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+=" sci-biology/clustal-omega" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch new file mode 100644 index 000000000000..5525d79b525f --- /dev/null +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f12ed19..b143922 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9135679..c201149 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-clustalomega/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/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest new file mode 100644 index 000000000000..74ca98eecf1d --- /dev/null +++ b/sci-biology/embassy-domainatrix/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domainatrix-0.1.0.tar.gz 420983 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1 +DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0 diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild new file mode 100644 index 000000000000..ee009ca052f0 --- /dev/null +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain analysis add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild new file mode 100644 index 000000000000..9734758ee2ad --- /dev/null +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain analysis add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..a932e1ebe21e --- /dev/null +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index d16cc02..d327a0d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d405d00..54be7ca 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domainatrix/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/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest new file mode 100644 index 000000000000..87fdc97be669 --- /dev/null +++ b/sci-biology/embassy-domalign/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domalign-0.1.0.tar.gz 462156 SHA256 c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a +DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37 diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild new file mode 100644 index 000000000000..8a0e7bb2de92 --- /dev/null +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain alignment add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild new file mode 100644 index 000000000000..b26dd2cb35df --- /dev/null +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain alignment add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..033ddf7b6535 --- /dev/null +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -0,0 +1,101 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 ++----- + 2 files changed, 9 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 693eb4d..dc0fda9 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 8785446..fe85f11 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domalign/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/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest new file mode 100644 index 000000000000..76709b452174 --- /dev/null +++ b/sci-biology/embassy-domsearch/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domsearch-0.1.0.tar.gz 470537 SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95 +DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111 diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild new file mode 100644 index 000000000000..48f945c08d8a --- /dev/null +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain search add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild new file mode 100644 index 000000000000..e9c4a6c48fd4 --- /dev/null +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain search add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..d24857c8386d --- /dev/null +++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f0f97fa..d419d7d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9829ebd..433a5c5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domsearch/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/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest new file mode 100644 index 000000000000..7c67122bbc0a --- /dev/null +++ b/sci-biology/embassy-emnu/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-emnu-1.05.tar.gz 390229 SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333 +DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild new file mode 100644 index 000000000000..3163cb635c4c --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +RDEPEND="sys-libs/ncurses + ${RDEPEND}" + +DEPEND="sys-libs/ncurses + ${DEPEND}" diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild new file mode 100644 index 000000000000..ee617cddf7ca --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Simple menu of EMBOSS applications" +EBO_EXTRA_ECONF="$(use_enable ncurses curses)" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +IUSE+=" ncurses" + +RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch new file mode 100644 index 000000000000..4e14bac1704a --- /dev/null +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -0,0 +1,139 @@ + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 +++--- + 3 files changed, 18 insertions(+), 58 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 7482ade..b815bdb 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -899,20 +864,16 @@ dnl fi + + + dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) + +-AC_MSG_CHECKING([for curses]) +- +-AS_IF([test "${with_curses}"], +-[ +- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +- LDFLAGS="$LDFLAGS -L${with_curses}/lib" ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++ PKG_CHECK_MODULES([FORM], [form]) ++ PKG_CHECK_MODULES([MENU], [menu]) + ]) + +-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"]) +- + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b295079..330c76f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \ ++ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS) + endif + + if ISSHARED +@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) ++ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-emnu/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/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest new file mode 100644 index 000000000000..ade72c4415f8 --- /dev/null +++ b/sci-biology/embassy-esim4/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 +DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild new file mode 100644 index 000000000000..927f8ab6a202 --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild new file mode 100644 index 000000000000..470cb0b299cd --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..ead54c91b5f3 --- /dev/null +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 924220a..2c45f46 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0620938..0304bb8 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-esim4/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/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest new file mode 100644 index 000000000000..1aeb5559decf --- /dev/null +++ b/sci-biology/embassy-hmmer/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-hmmer-2.3.2.tar.gz 565686 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258 +DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild new file mode 100644 index 000000000000..a246730c4b22 --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +RDEPEND="~sci-biology/hmmer-2.3.2" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/hmmer + doins src/*.h +} diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild new file mode 100644 index 000000000000..871d512a172a --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Wrappers for HMMER - Biological sequence analysis with profile HMMs" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+="sci-biology/hmmer" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch new file mode 100644 index 000000000000..90c45632eada --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 037ca00..f539ab6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index dc789bc..5a8c38e 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-hmmer/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/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest new file mode 100644 index 000000000000..6d689c8ee615 --- /dev/null +++ b/sci-biology/embassy-iprscan/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-iprscan-4.3.1.tar.gz 339939 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a +DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8 diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild new file mode 100644 index 000000000000..f8e7380c017c --- /dev/null +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="InterProScan motif detection add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild new file mode 100644 index 000000000000..2ed141470a13 --- /dev/null +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="InterProScan motif detection add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch new file mode 100644 index 000000000000..8c8a1060e30f --- /dev/null +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 9052ca5..c12c268 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0afc96a..904b41a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-iprscan/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/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest new file mode 100644 index 000000000000..13e38d3a79dd --- /dev/null +++ b/sci-biology/embassy-meme/Manifest @@ -0,0 +1 @@ +DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51 diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild new file mode 100644 index 000000000000..bdbc70a3bab2 --- /dev/null +++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Wrappers for MEME - Multiple Em for Motif Elicitation" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND+=" sci-biology/meme" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch new file mode 100644 index 000000000000..56f5814e1efa --- /dev/null +++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 391989f..d921f25 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1600399..9f28162 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-meme/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/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest new file mode 100644 index 000000000000..f42b89771c56 --- /dev/null +++ b/sci-biology/embassy-memenew/Manifest @@ -0,0 +1,2 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-memenew-0.1.0.tar.gz 450102 SHA256 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636 diff --git a/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild new file mode 100644 index 000000000000..58f3852fce08 --- /dev/null +++ b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/meme + doins src/INCLUDE/*.h +} diff --git a/sci-biology/embassy-memenew/metadata.xml b/sci-biology/embassy-memenew/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-memenew/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/embassy-mira/Manifest b/sci-biology/embassy-mira/Manifest new file mode 100644 index 000000000000..6229623c3b0e --- /dev/null +++ b/sci-biology/embassy-mira/Manifest @@ -0,0 +1,2 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-mira-2.8.2.tar.gz 365566 SHA256 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1 diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild new file mode 100644 index 000000000000..28e3d2587d1e --- /dev/null +++ b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Fragment assembly add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-mira/metadata.xml b/sci-biology/embassy-mira/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-mira/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/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest new file mode 100644 index 000000000000..15e2c00a0f43 --- /dev/null +++ b/sci-biology/embassy-mse/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90 +DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b diff --git a/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild new file mode 100644 index 000000000000..8767aee8f8d3 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Screen Editor" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild new file mode 100644 index 000000000000..32b6410620e1 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" +EBO_EXTRA_ECONF="$(use_enable ncurses curses)" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +IUSE+=" ncurses" + +RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) + +src_install() { + autotools-utils_src_install + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..c1095b266d60 --- /dev/null +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -0,0 +1,149 @@ + ckit/Makefile.am | 2 +- + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++--- + 4 files changed, 18 insertions(+), 59 deletions(-) + +diff --git a/ckit/Makefile.am b/ckit/Makefile.am +index f87b131..a670d2b 100644 +--- a/ckit/Makefile.am ++++ b/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +diff --git a/configure.ac b/configure.ac +index a20d488..eb208bf 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], + + + +-dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +- [AS_HELP_STRING([--with-curses], +- [curses (or ncurses)])]) +-if test "${with_curses}" ; then +-AC_MSG_CHECKING([for curses]) +-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +-LDFLAGS="$LDFLAGS -L${with_curses}/lib" +-fi +-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++]) + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b44632a..84e89b5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../h -I${embprefix}/include \ +- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ +- $(NLINCLUDES) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \ + $(XLIB) + else + LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-mse/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/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest new file mode 100644 index 000000000000..638f9da73ac0 --- /dev/null +++ b/sci-biology/embassy-phylipnew/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945 +DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58 diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild new file mode 100644 index 000000000000..2bc4a956502f --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild @@ -0,0 +1,14 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package" +LICENSE="freedist" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild new file mode 100644 index 000000000000..18b8b33c91fb --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="The Phylogeny Inference Package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +LICENSE+=" freedist" + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch new file mode 100644 index 000000000000..1cba944094a2 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -0,0 +1,111 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 ++----- + 3 files changed, 10 insertions(+), 48 deletions(-) + +diff --git a/configure.ac b/configure.ac +index e5bfaf1..09ed517 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1883ce9..fb1787f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-phylipnew/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/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest new file mode 100644 index 000000000000..8e615337acb6 --- /dev/null +++ b/sci-biology/embassy-signature/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-signature-0.1.0.tar.gz 574940 SHA256 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f +DIST embassy-signature-0.1.650.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3 diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild new file mode 100644 index 000000000000..83f7f8487ee8 --- /dev/null +++ b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein signature add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild new file mode 100644 index 000000000000..b70e05d76087 --- /dev/null +++ b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein signature add-on package" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) +AUTOTOOLS_AUTORECONF=1 +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..32e4d684cbb3 --- /dev/null +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 2f5ddd0..827543f 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d77e43c..849f17a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-signature/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/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest new file mode 100644 index 000000000000..7cd125ec2b29 --- /dev/null +++ b/sci-biology/embassy-structure/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 +DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild new file mode 100644 index 000000000000..64b653083ff2 --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein structure add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild new file mode 100644 index 000000000000..b6fcd9770e3b --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein structure add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..bdd9e37714e4 --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ee482ef..e4af4b1 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 81ade5d..2ed0d14 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-structure/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/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest new file mode 100644 index 000000000000..7da88ac0231b --- /dev/null +++ b/sci-biology/embassy-topo/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-topo-1.0.0.tar.gz 379929 SHA256 a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16 +DIST embassy-topo-2.0.650.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55 diff --git a/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild new file mode 100644 index 000000000000..f0ffdd356594 --- /dev/null +++ b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild new file mode 100644 index 000000000000..dec34b9db31f --- /dev/null +++ b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Transmembrane protein display" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch new file mode 100644 index 000000000000..3c37879de8c8 --- /dev/null +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 8eeb8ca..4fd28ac 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1cdb0b1..0e86a4b 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-topo/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/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest new file mode 100644 index 000000000000..d7061f3dd813 --- /dev/null +++ b/sci-biology/embassy-vienna/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db +DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2 diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild new file mode 100644 index 000000000000..62f1626a26a4 --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild new file mode 100644 index 000000000000..49eac3cdc4d8 --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of the Vienna RNA package - RNA folding" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch new file mode 100644 index 000000000000..5ce365ed5497 --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -0,0 +1,108 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 +++---- + 2 files changed, 10 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f5a4ecf..bbe0743 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -649,33 +649,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1f5b756..e178914 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF) + endif + + liboviennarna_la_LDFLAGS = $(LINKFLAGS) ++liboviennarna_la_LIBADD = -lajax + + ovrnaalifold_SOURCES = vrnaalifold.c + ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c +@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \ + $(XLIB) + else + LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-vienna/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/embassy/embassy-6.0.1.ebuild b/sci-biology/embassy/embassy-6.0.1.ebuild new file mode 100644 index 000000000000..3c7c37b20ff6 --- /dev/null +++ b/sci-biology/embassy/embassy-6.0.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://www.emboss.org/" +SRC_URI="" +LICENSE="GPL-2 freedist" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86" +IUSE="" + +RDEPEND="!<sci-biology/emboss-6.0.1 + !sci-biology/embassy-meme + !sci-biology/embassy-phylip + ~sci-biology/emboss-6.0.1 + =sci-biology/embassy-cbstools-1.0.0 + =sci-biology/embassy-domainatrix-0.1.0-r3 + =sci-biology/embassy-domalign-0.1.0-r3 + =sci-biology/embassy-domsearch-0.1.0-r3 + =sci-biology/embassy-emnu-1.05-r5 + =sci-biology/embassy-esim4-1.0.0-r5 + =sci-biology/embassy-hmmer-2.3.2-r2 + =sci-biology/embassy-iprscan-4.3.1 + =sci-biology/embassy-memenew-0.1.0-r1 + =sci-biology/embassy-mira-2.8.2 + =sci-biology/embassy-mse-1.0.0-r6 + =sci-biology/embassy-phylipnew-3.67 + =sci-biology/embassy-signature-0.1.0-r3 + =sci-biology/embassy-structure-0.1.0-r3 + =sci-biology/embassy-topo-1.0.0-r5 + =sci-biology/embassy-vienna-1.7.2" diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild new file mode 100644 index 000000000000..d663e22efda3 --- /dev/null +++ b/sci-biology/embassy/embassy-6.6.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://emboss.sourceforge.net/embassy/" + +LICENSE+=" freedist" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+=" + >=sci-biology/embassy-cbstools-1.0.0.650 + >=sci-biology/embassy-clustalomega-1.1.0 + >=sci-biology/embassy-domainatrix-0.1.650 + >=sci-biology/embassy-domalign-0.1.650 + >=sci-biology/embassy-domsearch-0.1.650 + >=sci-biology/embassy-emnu-1.05.650 + >=sci-biology/embassy-esim4-1.0.0.650 + >=sci-biology/embassy-hmmer-2.3.2.650 + >=sci-biology/embassy-iprscan-4.3.1.650 + >=sci-biology/embassy-meme-4.7.650 + >=sci-biology/embassy-mse-3.0.0.650 + >=sci-biology/embassy-phylipnew-3.69.650 + >=sci-biology/embassy-signature-0.1.650 + >=sci-biology/embassy-structure-0.1.650 + >=sci-biology/embassy-topo-2.0.650 + >=sci-biology/embassy-vienna-1.7.2.650 +" diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy/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/emboss/Manifest b/sci-biology/emboss/Manifest new file mode 100644 index 000000000000..c364f2c77e86 --- /dev/null +++ b/sci-biology/emboss/Manifest @@ -0,0 +1,4 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d +DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe +DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild new file mode 100644 index 000000000000..0edfd7a639d0 --- /dev/null +++ b/sci-biology/emboss/emboss-6.0.1.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=1 + +inherit eutils + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz" +LICENSE="GPL-2 LGPL-2" + +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="X png minimal" + +DEPEND=" + X? ( x11-libs/libXt ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + )" + +RDEPEND="${DEPEND} + !sys-devel/cons" + +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch + + local link_string="$(pkg-config --libs x11)" + if use png; then + link_string="${link_string} -lgd $(pkg-config --libs libpng)" + fi + sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ + || die "Failed to patch ajax Makefile" +} + +src_compile() { + local myconf + myconf="--includedir=${D}/usr/include/emboss" + use X || myconf="${EXTRA_CONF} --without-x" + use png || myconf="${EXTRA_CONF} --without-pngdriver" + + econf ${myconf} + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will eventually be available as a separate package. + sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ + Makefile || die + emake || die +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ + || die "Failed to install documentation." + newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ + || die "Failed to install Gentoo readme file." + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss || die "Failed to install environment file." + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die + + # Clashes #330507 + mv "${D}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild new file mode 100644 index 000000000000..e8baba4c7752 --- /dev/null +++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit autotools eutils + +MY_PATCH="4" + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI=" + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz" + +LICENSE="GPL-2 LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc minimal mysql pdf png postgres static-libs X" + +DEPEND=" + dev-libs/expat + dev-libs/libpcre:3 + sci-libs/plplot + sys-libs/zlib + mysql? ( virtual/mysql ) + pdf? ( media-libs/libharu ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + postgres? ( dev-db/postgresql ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + ) + X? ( x11-libs/libXt )" +RDEPEND="${DEPEND} + !sys-devel/cons" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}" + +src_prepare() { + epatch "${WORKDIR}"/${P}.patch + epatch \ + "${FILESDIR}"/${PV}-unbundle-libs.patch \ + "${FILESDIR}/${PF}_plcol.patch" + eautoreconf +} + +src_configure() { + econf \ + $(use_with X x) \ + $(use_with png pngdriver "${EPREFIX}/usr") \ + $(use_with doc docroot "${EPREFIX}/usr") \ + $(use_with pdf hpdf "${EPREFIX}/usr") \ + $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \ + $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \ + $(use_enable amd64 64) \ + $(use_enable static-libs static) \ + --without-java \ + --enable-large \ + --enable-systemlibs \ + --includedir="${ED}/usr/include/emboss" +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS + sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html + + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild new file mode 100644 index 000000000000..22d650f1107a --- /dev/null +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +inherit autotools-utils emboss-r1 eutils readme.gentoo + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" + +KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE+=" minimal" +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" + +RDEPEND+=" !sys-devel/cons" +PDEPEND+=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/primer3 + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + )" + +S="${WORKDIR}"/EMBOSS-${PV} + +DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) + +PATCHES=( + "${FILESDIR}"/${P}_fix-build-system.patch + "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch + "${FILESDIR}"/${P}_plplot-declarations.patch + "${FILESDIR}"/${P}_qa-implicit-declarations.patch +) + +src_install() { + # Use autotools-utils_* to remove useless *.la files + autotools-utils_src_install + + readme.gentoo_create_doc + + # Install env file for setting libplplot and acd files path. + cat > 22emboss <<- EOF + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + doenvd 22emboss + + # Remove useless dummy files + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." +} diff --git a/sci-biology/emboss/files/22emboss b/sci-biology/emboss/files/22emboss new file mode 100644 index 000000000000..177643ced11f --- /dev/null +++ b/sci-biology/emboss/files/22emboss @@ -0,0 +1,4 @@ +# plplot libs dir +PLPLOT_LIB="/usr/share/EMBOSS/" +# ACD files location +EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" diff --git a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch new file mode 100644 index 000000000000..5e463744a739 --- /dev/null +++ b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch @@ -0,0 +1,600 @@ +diff --git a/Makefile.am b/Makefile.am +index 4fe2ed1..7f3a95f 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4 + + AUTOMAKE_OPTIONS = gnits + +-SUBDIRS = plplot ajax nucleus emboss test doc jemboss ++if !ESYSTEMLIBS ++EXTRA_DIRS = plplot ++endif ++ ++if GJEMBOSS ++JEMBOSS_DIR = jemboss ++endif ++ ++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) ++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) + + # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" + + # files with nonstandard names in this directory +-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh ++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh + + # tar to pick up the other directories + # then remove any CVS subdirectories +diff --git a/README.fixes b/README.fixes +new file mode 100644 +index 0000000..3c56d79 +--- /dev/null ++++ b/README.fixes +@@ -0,0 +1,9 @@ ++The files in this directory are bugfix replacements for files in ++the EMBOSS-6.3.1 distribution. Just drop the replacement files in ++the location shown and redo the 'make install.' ++ ++Fix 1. EMBOSS-6.3.1/configure ++ EMBOSS-6.3.1/m4/mysql.m4 ++ ++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of ++ hpdf support prevented inclusion of MySQL support. +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index 4a44f6f..cf27ff8 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,6 +1,6 @@ + ## Process this file with automake to produce Makefile.in + if !ESYSTEMLIBS +-EXTRA_DIRS = expat zlib ++EXTRA_DIRS = pcre expat zlib + endif + +-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd ++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 02bcaa7..368ddfe 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am +@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/ajax/graphics \ +@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libacd_la_LDFLAGS = $(LINKFLAGS) ++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index da57727..857ca5f 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am +@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl + +@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxdb_la_LDFLAGS = $(LINKFLAGS) ++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index af27cb0..8fa4a3a 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_LIBS = -lexpat -lpcre + endif + ++EXTRA_DIST = ajax-pcre-config.h.in ++DISTCLEAN = ajax-pcre-config.h + + INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ + -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ +--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) ++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS) + + AJAXSRC = ajalign.c ajarr.c ajassert.c \ + ajbase.c ajcall.c ajcod.c \ +@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \ + ajmath.h ajmatrices.h ajmem.h ajmess.h \ + ajnam.h ajnexus.h ajobo.h \ + ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ +-ajrange.h ajreg.h ajreport.h ajresource.h \ ++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \ + ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \ + ajsort.h ajsql.h ajstr.h ajsys.h \ + ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h +@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajax_la_LDFLAGS = $(LINKFLAGS) ++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS) +diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in +new file mode 100644 +index 0000000..b09e4e6 +--- /dev/null ++++ b/ajax/core/ajax-pcre-config.h.in +@@ -0,0 +1 @@ ++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 06793be..659f462 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -16,9 +16,14 @@ extern "C" + #define ajreg_h + + #include "ajax.h" ++#include "ajax-pcre-config.h" ++#ifndef AJAX_USE_SYSTEM_PCRE + #include "pcre_config.h" + #include "pcre_internal.h" + #include "pcreposix.h" ++#else ++#include <pcre.h> ++#endif + + #define AJREG_OVECSIZE 30 + +@@ -41,7 +46,11 @@ extern "C" + ******************************************************************************/ + + typedef struct AjSRegexp { ++#ifndef AJAX_USE_SYSTEM_PCRE + real_pcre *pcre; ++#else ++ pcre *pcre; ++#endif + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index ca33a84..87e51bd 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \ +--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core ++INCLUDES = $(EXTRA_INCLUDES) \ ++-I$(top_srcdir)/ajax/core + + ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \ + ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \ +@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libensembl_la_LDFLAGS = $(LINKFLAGS) ++libensembl_la_LIBADD = ../core/libajax.la +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index ab45afc..f61c605 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am +@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM ++EXTRA_LIBS = $(PLPLOT_LIBS) + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core + + AJAXGSRC = ajgraph.c ajhist.c +@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxg_la_LDFLAGS = $(LINKFLAGS) ++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) +diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c +index 25e75e4..60f2743 100644 +--- a/ajax/graphics/ajgraph.c ++++ b/ajax/graphics/ajgraph.c +@@ -34,10 +34,8 @@ + #include <float.h> + #define AZ 28 + +- + #include "plplotP.h" + +- + static void GraphArray(ajuint numofpoints, + float *x, float *y); + static void GraphArrayGaps(ajuint numofpoints, +@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) + ** @@ + ******************************************************************************/ + ++#define _GNU_SOURCE ++#include <stdio.h> ++ + static void GraphSetName(const AjPGraph thys, + const AjPStr txt, const char *ext) + { + if(!thys->ready) + { ++#ifdef USE_PLXSFNAM_SHIM ++ char *fullname; ++#endif + ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++#ifdef USE_PLXSFNAM_SHIM ++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); ++ ajDebug("=g= plsfnam ('%S') instead\n", fullname); ++ plsfnam(fullname); ++ free(fullname); ++#else + plxsfnam(ajStrGetPtr(txt), ext); ++#endif + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +diff --git a/configure.in b/configure.in +index ddb4f81..3f4fe5e 100644 +--- a/configure.in ++++ b/configure.in +@@ -235,15 +235,6 @@ AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_MAKE_SET + +-dnl Intel MacOSX 10.6 puts X11 in a non-standard place +-if test "${with_x}" != "no" ; then +-if test "`uname -a | grep Darwin`"; then +-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` +-if test ${OSXX} '>' '10.4'; then +-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" +-fi +-fi +-fi + + # Checks for header files. + #as# AC_PATH_X +@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove) + #as# select socket sqrt strchr strcspn strdup strerror strpbrk \ + #as# strrchr strspn strstr strtol]) + +-if test "${with_x}" != "no" ; then +-LF_EMBOSS_PATH_XLIB +-fi + + dnl Library checks + AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") +@@ -316,14 +304,16 @@ CHECK_PNGDRIVER + CHECK_AUTH + CHECK_AMD64 + ++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes") ++ + AX_LIB_MYSQL + AX_LIB_POSTGRESQL + + CFLAGS="$CFLAGS $MYSQL_CFLAGS" + LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" + +-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" +-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" ++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" ++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS" + + + dnl Check for 'ant' for packaging Jemboss and export result +@@ -443,13 +433,36 @@ fi + + dnl Test if --enable-systemlibs given + have_systemlibs=no ++DEFINE_USE_SYSTEM_PCRE="#undef" + AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])) ++AC_MSG_CHECKING(for systemlib usage) + if test "${enable_systemlibs}" = "yes" ; then + have_systemlibs=yes ++ DEFINE_USE_SYSTEM_PCRE="#define" ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++else ++ dnl X11 is only used by plplot ++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place ++ if test "${with_x}" != "no" ; then ++ if test "`uname -a | grep Darwin`"; then ++ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` ++ if test ${OSXX} '>' '10.4'; then ++ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" ++ fi ++ fi ++ fi ++ if test "${with_x}" != "no" ; then ++ LF_EMBOSS_PATH_XLIB ++ fi ++ AC_MSG_NOTICE(USING bundled LIBS) + fi + AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") + AC_SUBST(ESYSTEMLIBS) ++AC_SUBST(DEFINE_USE_SYSTEM_PCRE) ++AC_SUBST(PLPLOT_CFLAGS) ++AC_SUBST(PLPLOT_LIBS) + + + +@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS) + + dnl Test if purify exists and if --enable-purify given if so + dnl set "-g" +- + AC_MSG_CHECKING(for purify) + dnl if(purify -version) < /dev/null > /dev/null 2>&1; then + AC_ARG_ENABLE(purify, +@@ -683,6 +695,7 @@ CHECK_THREADS + + + AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ++ajax/core/ajax-pcre-config.h + ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile + ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile + ajax/acd/Makefile +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 0820517..a0257b2 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \ + yank + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = -I$(top_srcdir)/nucleus \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot ++ -I$(top_srcdir)/ajax/acd + + + aaindexextract_SOURCES = aaindexextract.c +@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c + treetypedisplay_SOURCES = treetypedisplay.c + + if !ESYSTEMLIBS +-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la + endif + + +@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ + ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ + ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ + $(EXTRA_LDS) \ +- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ + $(XLIB) + + pkgdata_DATA = emboss.default.template +diff --git a/m4/mysql.m4 b/m4/mysql.m4 +index fe413af..ebea25c 100644 +--- a/m4/mysql.m4 ++++ b/m4/mysql.m4 +@@ -1,4 +1,6 @@ +-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html ++# =========================================================================== + # + # SYNOPSIS + # +@@ -6,19 +8,18 @@ + # + # DESCRIPTION + # +-# This macro provides tests of availability of MySQL client library +-# of particular version or newer. ++# This macro provides tests of availability of MySQL client library of ++# particular version or newer. + # +-# AX_LIB_MYSQL macro takes only one argument which is optional. If +-# there is no required version passed, then macro does not run +-# version test. ++# AX_LIB_MYSQL macro takes only one argument which is optional. If there ++# is no required version passed, then macro does not run version test. + # + # The --with-mysql option takes one of three possible values: + # + # no - do not check for MySQL client library + # +-# yes - do check for MySQL library in standard locations +-# (mysql_config should be in the PATH) ++# yes - do check for MySQL library in standard locations (mysql_config ++# should be in the PATH) + # + # path - complete path to mysql_config utility, use this option if + # mysql_config can't be found in the PATH +@@ -33,27 +34,23 @@ + # + # HAVE_MYSQL + # +-# LAST MODIFICATION ++# LICENSE + # +-# 2006-07-16 +-# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers, +-# which prevents gdb from displaying stack traces. +-# Changed mysql_config --cflags to mysql_config --include ++# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net> + # +-# COPYLEFT +-# +-# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net> +-# +-# Copying and distribution of this file, with or without +-# modification, are permitted in any medium without royalty provided +-# the copyright notice and this notice are preserved. ++# Copying and distribution of this file, with or without modification, are ++# permitted in any medium without royalty provided the copyright notice ++# and this notice are preserved. This file is offered as-is, without any ++# warranty. ++ ++#serial 12 + + AC_DEFUN([AX_LIB_MYSQL], + [ + AC_ARG_WITH([mysql], +- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], ++ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], + [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] +- )], ++ ), + [ + if test "$withval" = "no"; then + want_mysql="no" +@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL], + ], + [want_mysql="yes"] + ) ++ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) + + MYSQL_CFLAGS="" + MYSQL_LDFLAGS="" + MYSQL_VERSION="" + + dnl +- dnl Check MySQL libraries (libpq) ++ dnl Check MySQL libraries + dnl + + if test "$want_mysql" = "yes"; then + +- if test -z "$MYSQL_CONFIG" -o test; then +- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no]) ++ if test -z "$MYSQL_CONFIG" ; then ++ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) + fi + + if test "$MYSQL_CONFIG" != "no"; then +@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" + + MYSQL_VERSION=`$MYSQL_CONFIG --version` + +-dnl It isn't enough to just test for mysql_config as Fedora +-dnl provides it in the mysql RPM even though mysql-devel may +-dnl not be installed +- +- EMBCFLAGS=$CFLAGS +- EMBLDFLAGS=$LDFLAGS +- CFLAGS=$MYSQL_CFLAGS +- LDFLAGS=$MYSQL_LDFLAGS +- +- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h> +- #include "mysql.h"]], +- [[mysql_info(NULL)]])], +- [havemysql=yes], +- [havemysql=no]) +- +- CFLAGS=$EMBCFLAGS +- LDFLAGS=$EMBLDFLAGS +- +- if test "$havemysql" = yes; then +- AC_DEFINE([HAVE_MYSQL], [1], +- [Define to 1 if MySQL libraries are available]) +- found_mysql="yes" +- AC_MSG_RESULT([yes]) +- else +- MYSQL_CFLAGS="" +- MYSQL_LDFLAGS="" +- found_mysql="no" +- AC_MSG_RESULT([no]) +- fi |