Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sci-biology/lastz: A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement
  sci-biology/YASRA: Yet Another Short Read Assembler to reference using LASTZ
  sci-biology/gbrowse: added dev-perl/TermReadKey to dependencies
  sci-biology/libgtextutils: Gordon text utils library
  [dev-libs/fortrancl] initial import, ebuild written by me

19 files changed, 352 insertions, 13 deletions

diff --git a/dev-libs/fortrancl/Manifest b/dev-libs/fortrancl/Manifest
new file mode 100644
index 000000000..f86dc2714
--- /dev/null
+++ b/dev-libs/fortrancl/Manifest
@@ -0,0 +1 @@
+DIST fortrancl-0.1alpha2.tar.gz 139478 SHA256 711fdab1b377674089a821954aa2164fea6800740e86c70779ac57938a138d92 SHA512 c2569672a26926bda8fa1a716cd7909403c0892f6f2acf7abc4e9b62f3d42fc9807de4c9554414146120f6531bae06c0a585cd034d84ac8faf11197f8f927ba4 WHIRLPOOL ce8a9a053b7abfe67d1882b3ea883f31bb5ee99052e44b22b73f6206e9c49d545d1e1812ac4caa712ffcf4777519e7a159e9385d3d49a4aadfb62eba6400b491
diff --git a/dev-libs/fortrancl/files/fortrancl-0.1_alpha2-gentoo.patch b/dev-libs/fortrancl/files/fortrancl-0.1_alpha2-gentoo.patch
new file mode 100644
index 000000000..f31969d08
--- /dev/null
+++ b/dev-libs/fortrancl/files/fortrancl-0.1_alpha2-gentoo.patch
@@ -0,0 +1,144 @@
+Index: src/Makefile.am
+===================================================================
+--- src/Makefile.am	(wersja 129)
++++ src/Makefile.am	(kopia robocza)
+@@ -23,11 +23,12 @@
+   LIBFUNCMOD = cl.@ax_cv_f90_modext@
+ endif
+ 
+-nodist_include_HEADERS = $(LIBFUNCMOD)
++fortrancl_includedir = $(includedir)/fortrancl
++nodist_fortrancl_include_HEADERS = $(LIBFUNCMOD)
+ 
+-lib_LIBRARIES = libfortrancl.a
++lib_LTLIBRARIES = libfortrancl.la
+ 
+-libfortrancl_a_SOURCES =       \
++libfortrancl_la_SOURCES =       \
+ 	cl_types.f90           \
+ 	cl_buffer.f90          \
+ 	cl_command_queue.f90   \
+@@ -39,7 +40,7 @@
+ 	cl_program.f90         \
+ 	cl.f90
+ 
+-libfortrancl_a_SOURCES +=            \
++libfortrancl_la_SOURCES +=            \
+ 	cl_buffer_low.c              \
+ 	cl_command_queue_low.c       \
+ 	cl_context_low.c             \
+@@ -51,15 +52,17 @@
+ noinst_HEADERS =               \
+ 	string_f.h
+ 
+-cl_types.o     : cl_types.f90 
+-cl_constants.o : cl_constants.f90
+-cl_platform.o  : cl_platform.f90 cl_types.o 
+-cl_program.o   : cl_program.f90 cl_types.o 
+-cl_kernel.o    : cl_kernel.f90 cl_types.o 
+-cl_device.o    : cl_device.f90 cl_types.o 
+-cl_context.o   : cl_context.f90 cl_types.o 
+-cl_command_queue.o : cl_command_queue.f90 cl_types.o 
+-cl_buffer.o    : cl_buffer.f90  cl_types.o 
+-cl.o : cl.f90 cl_constants.o cl_types.o cl_device.o cl_kernel.o cl_program.o cl_platform.o cl_context.o cl_command_queue.o cl_buffer.o
++$(LIBFUNCMOD):   cl.lo
+ 
++cl_types.lo     : cl_types.f90 
++cl_constants.lo : cl_constants.f90
++cl_platform.lo  : cl_platform.f90 cl_types.lo 
++cl_program.lo   : cl_program.f90 cl_types.lo 
++cl_kernel.lo    : cl_kernel.f90 cl_types.lo 
++cl_device.lo    : cl_device.f90 cl_types.lo 
++cl_context.lo   : cl_context.f90 cl_types.lo 
++cl_command_queue.lo : cl_command_queue.f90 cl_types.lo 
++cl_buffer.lo    : cl_buffer.f90  cl_types.lo 
++cl.lo : cl.f90 cl_constants.lo cl_types.lo cl_device.lo cl_kernel.lo cl_program.lo cl_platform.lo cl_context.lo cl_command_queue.lo cl_buffer.lo
++
+ CLEANFILES = *~ *.bak *.mod *.MOD *.il *.d *.pc* ifc*
+Index: configure.ac
+===================================================================
+--- configure.ac	(wersja 129)
++++ configure.ac	(kopia robocza)
+@@ -32,11 +32,16 @@
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+-AC_PROG_RANLIB
+ AC_PROG_YACC
+ 
+ AC_PROG_CC
++LT_INIT([disable-static])
+ 
++# Set proper version
++# http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
++AC_SUBST([FORTRANCL_SO_VERSION], [0:0:0])
++#AC_SUBST([FORTRANCL_API_VERSION], [1.1])   # set to proper API OpenCL version
++
+ # Checks for header files.
+ AC_HEADER_STDC
+ 
+@@ -73,8 +78,9 @@
+ AC_SUBST(ax_cv_f90_modext)
+ AM_CONDITIONAL(F90_MOD_UPPERCASE, [test x$ax_f90_mod_uppercase = xyes])
+ 
+-AC_CONFIG_FILES([Makefile])
+-AC_CONFIG_FILES([src/Makefile])
+-AC_CONFIG_FILES([examples/Makefile])
++AC_CONFIG_FILES([Makefile
++                 src/Makefile
++                 examples/Makefile
++                 fortrancl.pc])
+ 
+ AC_OUTPUT
+Index: fortrancl.pc.in
+===================================================================
+--- fortrancl.pc.in	(wersja 0)
++++ fortrancl.pc.in	(kopia robocza)
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: OpenCL interface for Fortran 90
++Version: @PACKAGE_VERSION@
++URL: @PACKAGE_URL@
++Libs: -L${libdir} -lfortrancl
++Cflags: -I${includedir}/fortrancl
+Index: Makefile.am
+===================================================================
+--- Makefile.am	(wersja 129)
++++ Makefile.am	(kopia robocza)
+@@ -17,6 +17,12 @@
+ ##
+ ## $Id$
+ 
++ACLOCAL_AMFLAGS = -I m4
++
+ SUBDIRS = src examples
+ 
+-CLEANFILES = *~ *.bak *.mod *.MOD *.il *.d *.pc* ifc*
++CLEANFILES = *~ *.bak *.mod *.MOD *.il *.d *.pc ifc*
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = fortrancl.pc
++
+Index: examples/Makefile.am
+===================================================================
+--- examples/Makefile.am	(wersja 129)
++++ examples/Makefile.am	(kopia robocza)
+@@ -20,11 +20,11 @@
+ noinst_PROGRAMS = sum devices
+ 
+ sum_SOURCES = sum.f90
+-sum_LDADD = $(top_builddir)/src/libfortrancl.a
++sum_LDADD = $(top_builddir)/src/libfortrancl.la
+ dist_noinst_DATA = sum.cl
+ 
+ devices_SOURCES = devices.f90
+-devices_LDADD = $(top_builddir)/src/libfortrancl.a
++devices_LDADD = $(top_builddir)/src/libfortrancl.la
+ 
+ AM_FCFLAGS = @F90_MODULE_FLAG@$(top_builddir)/src
+ 
diff --git a/dev-libs/fortrancl/fortrancl-0.1_alpha2.ebuild b/dev-libs/fortrancl/fortrancl-0.1_alpha2.ebuild
new file mode 100644
index 000000000..09ebd9338
--- /dev/null
+++ b/dev-libs/fortrancl/fortrancl-0.1_alpha2.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+AUTOTOOLS_AUTORECONF=1
+
+inherit autotools-utils fortran-2
+
+MY_PV=${PV/_}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="OpenCL interface for Fortran 90"
+HOMEPAGE="http://code.google.com/p/fortrancl/"
+SRC_URI="http://${PN}.googlecode.com/files/${MY_P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="examples static-libs"
+
+DEPEND="virtual/opencl"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${MY_P}
+
+DOCS=( AUTHORS ChangeLog README )
+PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
+
+src_install() {
+ 	autotools-utils_src_install
+	if use examples ; then
+		insinto /usr/share/doc/${PF}/examples
+		doins examples/*.{f90,cl}
+	fi
+}
diff --git a/dev-libs/fortrancl/metadata.xml b/dev-libs/fortrancl/metadata.xml
new file mode 100644
index 000000000..626f07372
--- /dev/null
+++ b/dev-libs/fortrancl/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<maintainer>
+		<email>xarthisius@gentoo.org</email>
+		<name>Kacper Kowalik</name>
+	</maintainer>
+	<longdescription>
+		FortranCL is an OpenCL interface for Fortran 90. It allows programmers to call
+		the OpenCL parallel programming framework directly from Fortran, so developers
+		can accelerate their Fortran code using graphical processing units (GPU) and
+		other accelerators.
+		The interface is designed to be as close to C OpenCL interface as possible,
+		while written in native Fortran 90 with type checking. It was originally
+		designed as an OpenCL interface to be used by the Octopus code.
+		The interface is not complete but provides all the basic calls required to 
+		write a full Fortran 90 OpenCL program. 
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog
new file mode 100644
index 000000000..17ca0d95f
--- /dev/null
+++ b/sci-biology/YASRA/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/YASRA
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*YASRA-2.1 (17 Jan 2012)
+
+  17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +YASRA-2.1.ebuild,
+  +metadata.xml:
+  initial ebuild
+
diff --git a/sci-biology/YASRA/Manifest b/sci-biology/YASRA/Manifest
new file mode 100644
index 000000000..4c218feef
--- /dev/null
+++ b/sci-biology/YASRA/Manifest
@@ -0,0 +1 @@
+DIST YASRA-2.1.tar.gz 11949120 SHA256 d196cea91a69db3d2feb98d3a8dddbfe1c4c9b4689cdc706a58df44daba3d2d5 SHA512 1e5c648042b8c522c708eb80b90f5a7e965b4f0214a732ba19a46d826ea85bd7074946a2355e509df1ce1dfcec1700c7c6f3ad08c7052f754fed6241c078ec5b WHIRLPOOL 4419ce639b2afb95013b8896b059c037100dc58dc1664b2416ed05c68fd3fcce4eca01219dfa59874a26d566e1df393e975c8d6132811591a251f1acc3db00a4
diff --git a/sci-biology/YASRA/YASRA-2.1.ebuild b/sci-biology/YASRA/YASRA-2.1.ebuild
new file mode 100644
index 000000000..3c3e10d58
--- /dev/null
+++ b/sci-biology/YASRA/YASRA-2.1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Yet Another Short Read Assembler aligning to a reference using LASTZ"
+HOMEPAGE="http://www.bx.psu.edu/miller_lab/"
+SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-"${PV}".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-biology/lastz"
+
+S="${WORKDIR}"/YASRA
+
+src_install(){
+	emake install DESTDIR="$D"
+}
diff --git a/sci-biology/YASRA/metadata.xml b/sci-biology/YASRA/metadata.xml
new file mode 100644
index 000000000..07b525505
--- /dev/null
+++ b/sci-biology/YASRA/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>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b64e88094..c63914ae5 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/gbrowse
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
 
+  17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  gbrowse-2.39.ebuild:
+  added dev-perl/TermReadKey to dependencies
+
   30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch,
   +files/gbrowse_metadb_config.pl.patch, +files/symlink.patch:
diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest
index a1d806801..5d79df93e 100644
--- a/sci-biology/gbrowse/Manifest
+++ b/sci-biology/gbrowse/Manifest
@@ -1,11 +1,11 @@
-DIST GBrowse-2.39.tar.gz 11969088 RMD160 47dd338a0b99632e77a532a3c27d0b9d9d514dca SHA1 2cc48cc1603aa3ae487c47259f9a896bec4eff8e SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44
-DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a
-DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af
-DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea
-DIST fly.gff.gz 18687640 RMD160 fb54c40dd9508d2f9e9cf24b65195cfbb70c8f82 SHA1 2d77f89f438b389fee7e7f5c92fc902eb1f99482 SHA256 db03b56993b739dd6e6df92dcb94163f04ca03a1911c99dd4df4fe65e16b6d44
-DIST human.gff.tar.gz 40362676 RMD160 ae0bb58667d01ebc4c0a34ede4d4b1c347bc42be SHA1 6d71aba7ef054291021bc340571c253ec71cd60f SHA256 7d0ea6363e6dda8618f53b42dea72d6ef6034b4f2fb541b94b4800383009f6b0
-DIST saccharomyces_cerevisiae.gff.bz2 4000445 RMD160 133a9076971958d4a242b6fc10869056c169e53e SHA1 8ef80023a0ccdc714742b628873ab06f06f0ebe4 SHA256 fb41705b64f0e36cbb46fb6b7557c2f36e517db582f1472d852f89b46ca750d4
-DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 ef8237f08b8380ce72c3c067120893087bc3bd21 SHA256 dbd6dcc44a8960e0e475b0be31b03caa3d97f4ddfc36ba566862732880f7dbc0
-DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f
-DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d
-DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1
+DIST GBrowse-2.39.tar.gz 11969088 SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44 SHA512 4297192236a297a4f6a25892e245e3f5a4951b561ae167d7d402ff09b50a9a8a0d924094136d191d9068f735f77795a166e37aac67cd964d70cc805a15f8c26d WHIRLPOOL a0fc2c882d9e11f76d739a824152f9b5482f2b352583dc2e92fcfb60cf1b19ff1a9684c543ee6b8e69b3ed441548d5dd9b1d2da9e8779f0d157a7fe73f6e7af8
+DIST README-gff-files 5309 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a SHA512 b591d269400c28f8908e5cc7bd27815b35b1750661cd4bb2c34e94f712ce100f71c7e9934800477425747e75fdd487192c3a2c05cf7249e28006c986feb54cca WHIRLPOOL f4080b582ac52adc76536cb7dcd646e4ce85b0f8210ef2010e037db7d114b436077f3b7d7d84216030e92130ad5be649442ece1e281273b13c39c537542270b6
+DIST Refseq_Genome_TBLASTX.tar.gz 56482234 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af SHA512 d49dc91f1246a881acf1b4fa0f336fe25ee0317f04a5bc42f2750509f95af3768eabfa0d4517f97ee14bb5de9e59700e0a7ef9018e577d2a87874809d313fdfb WHIRLPOOL 0cc86c1987d5399b952ba05cb441035a03ef5e47242e7f2ce95a73cc5420ff8b581ab6b097b66c96d65dc73b9ef4e301473b89a29c60413dd4d4d5e39508b6df
+DIST fly.fasta.gz 37349852 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea SHA512 f3c0864d82be03c5e06a2e420ecd42df254318b7ee18f7dbb982b1c716ff5db465da69991ab009cf157b6a3601220fadd58d91d68732570af453e2bd329e09b7 WHIRLPOOL e914a4082913fff82687b0282e9ddcb01cfdd50712dbc30dba9ba697fcacc2b4b168f2b6b587479c84e2b51370ea7285fb6c5a8ce3961a55f3ee2ee29f27d169
+DIST fly.gff.gz 18687640 SHA256 db03b56993b739dd6e6df92dcb94163f04ca03a1911c99dd4df4fe65e16b6d44 SHA512 7f4ac316c4028d0e15c4b304169c7225379ad0857d4e66a0c03c1479eabe9beac84098786725b2895a12c607e2895492c24c920d85ba8c589c0d2e65d88bf687 WHIRLPOOL 4b2d66953afb33e9d6cafc7f6220a573129a8cdca49cadee089ed528faf55209d25bf5a8c82592c38248a5fa9bed205060d68dec853fe7b141b9bb1f00b816fa
+DIST human.gff.tar.gz 40362676 SHA256 7d0ea6363e6dda8618f53b42dea72d6ef6034b4f2fb541b94b4800383009f6b0 SHA512 c757d3573774a4328c4dbc564a3f9d0e415265fec788fbfcd1b1adcb93f4c58aebd02c26a01cad27de4d23a2b9a27f9099192580269e5c499e681336b056a648 WHIRLPOOL ed7847f7b7db34071ec4224b9f6d9fa70b42e0f15af2e5dc2df5b96520addc0cd6edfd106a6d6e1dec42f944de768ddd0a80929645f0e0d682cc6c625d165e2d
+DIST saccharomyces_cerevisiae.gff.bz2 4000445 SHA256 fb41705b64f0e36cbb46fb6b7557c2f36e517db582f1472d852f89b46ca750d4 SHA512 128c33a956e6b01b704bd37d21eebb123283fe3e2b1b7097158b4e0f6d951bca473d4dba5f03c902bf03d7a25e1ee2fdb22e2d829cfe39ee89d4c772825a41b4 WHIRLPOOL 1e1dc5114f22db8641feb933f5718b07afb8718e40afe8c9cd347280d598a12104c4396859f3a6dce96a12a640ca5452a08701f72126d9877eefab29b5177f2c
+DIST worm.fasta.gz 30593662 SHA256 dbd6dcc44a8960e0e475b0be31b03caa3d97f4ddfc36ba566862732880f7dbc0 SHA512 2518970a420d8f18cde0271fc9f1fe81cbce0f888bec9afe98497cc5389ea7a5a9d232a102ad776b2ecad8e29839f468ca06db3fc6babd13b6af5afa5843f0d1 WHIRLPOOL 744651e5f1ea1e7f5893db9b7e1114c42686fa70e27735c96ff828e4a061cba5cd95ddeba9f81dd0279213485d12c373ea0eb06dc8d0367cfdcb82556ea4101d
+DIST worm.gff.gz 65789458 SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f SHA512 9fde867eb2e676904bc79432ec3e293d69e6795fd7f18fa1de409c48417ba974dfe1ebc1c1c07c4825b83cd738c153de7b192da77b2c4a518131797984a608ca WHIRLPOOL 38d8c9965341824dcc561acc7670d21c5dba93c52efc0b1022f28e9f37eb986799a9e368537ce3a7c40c890a21b237025132012a43ebb860bbceb59624bd193d
+DIST yeast.fasta.gz 3801757 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d SHA512 5dc0a0ca99ff7fab859eec60df896dbdf6e6c20352ed2b88bf331b351442136a71a5d4adc0654be090e322c35ae20e1ea74286410b3c0f90dce6d89ad5170381 WHIRLPOOL 92e192cc027045ffbbfbc78fffa7a1f190b75026d4f1bd0061f1b3e3eb15c8b724ce566abd6f7bda48f5f941f870288a0a394625177d66beabd251bcfd479985
+DIST yeast.gff.gz 249814 SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 SHA512 2a4257569145a9d0d4c9d6b91e01c4f88771d2cc3c16ece9d0d86106903528e8c5386d51298c9360e9d59cfec21a6f61c6bc0b464d0561af6c18f6b2094fba8a WHIRLPOOL e17689198aa3710e02e090ddc38c6f7286d1e09e11ee88248e760053e23b33e0aacf88fcc594fec904fa520e3df55008db568147517c1a059ed7fe22896f8e1c
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index d4cee63ef..7f8ab9b0a 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 EAPI="2"
@@ -46,6 +46,7 @@ DEPEND="
 	dev-perl/Statistics-Descriptive
 	>=dev-perl/Bio-Graphics-1.97
 	>=dev-perl/JSON-2.510.0
+	dev-perl/TermReadKey
 	dev-perl/libwww-perl
 	svg? ( dev-perl/GD-SVG )
 	pdf? ( media-gfx/inkscape )
diff --git a/sci-biology/lastz/ChangeLog b/sci-biology/lastz/ChangeLog
new file mode 100644
index 000000000..8c73100f2
--- /dev/null
+++ b/sci-biology/lastz/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/lastz
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*lastz-1.02.00 (16 Jan 2012)
+
+  16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +lastz-1.02.00.ebuild, +metadata.xml:
+  initial ebuild
+
diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest
new file mode 100644
index 000000000..d9ecafa01
--- /dev/null
+++ b/sci-biology/lastz/Manifest
@@ -0,0 +1,2 @@
+DIST lastz-1.02.00.tar.gz 1827527 SHA256 054515f27fdf9392f3d2e84ca421103b5e5575ba7a1979addf3c277212114a21 SHA512 5507f511b98ee3d90af08120c6a41b6606c1c71f458c043f4ee85e2ff8108fb2d02b31c347fd6f211b49fb97aeac0ff1ed5f96895644c7cd94918ac57073ee0c WHIRLPOOL 242a9fecaf57b71b2c3a50033a01e9f12083bc56e3c9945102d8a789f0d4476d0c66ea2b78ce870e914f095409bb1c3b7ac3a5fbee94c7a59a05e351786a22d5
+DIST lav_format.html 11901 SHA256 81949a94b4864481cd1c48c4fac413765ada74b6f5b8a9577684399af8472408 SHA512 93fc8d7b45f893beebb23ff2be10d4352691c6bd93b9ecc5750fdd37f10038f91a644f57e95653b9138e14a2344e124d3ca543e0beeabc5fa922194374659b96 WHIRLPOOL 403110222223787abaa0034a1496f63b5cf115a3abeb9609e77130545ff4d1fbf6193909a820b25e78e011bd5f0340171b82a11e928bc7a8900377674c49b3e2
diff --git a/sci-biology/lastz/lastz-1.02.00.ebuild b/sci-biology/lastz/lastz-1.02.00.ebuild
new file mode 100644
index 000000000..233691f6d
--- /dev/null
+++ b/sci-biology/lastz/lastz-1.02.00.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement"
+HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
+SRC_URI="http://www.bx.psu.edu/miller_lab/dist/lastz-"${PV}".tar.gz
+		http://www.bx.psu.edu/miller_lab/dist/lav_format.html"
+
+LICENSE=""
+SLOT="0"
+#KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/lastz-distrib-"${PV}"
+
+src_install(){
+	dobin src/lastz src/lastz_D
+	dodoc README.lastz.html
+	dodoc "${DISTDIR}"/lav_format.html
+}
diff --git a/sci-biology/lastz/metadata.xml b/sci-biology/lastz/metadata.xml
new file mode 100644
index 000000000..07b525505
--- /dev/null
+++ b/sci-biology/lastz/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>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/libgtextutils/ChangeLog b/sci-biology/libgtextutils/ChangeLog
new file mode 100644
index 000000000..f36091b3d
--- /dev/null
+++ b/sci-biology/libgtextutils/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/libgtextutils
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*libgtextutils-0.6 (16 Jan 2012)
+
+  16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +libgtextutils-0.6.ebuild, +metadata.xml:
+  initial ebuild
+
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest
new file mode 100644
index 000000000..00e64b58f
--- /dev/null
+++ b/sci-biology/libgtextutils/Manifest
@@ -0,0 +1 @@
+DIST libgtextutils-0.6.tar.bz2 271032 SHA256 5c8a795a80134f0f8bdc62a92b5baf32eb689e40c9fc685c491c648eff5a30ba SHA512 26014853898583705c0d6693e2ac7adc49e1218cd07109b25c7392514e1899d772bb0ee01cd27bd1ceada0072c53536ba04082b9dc7f3b1822a206f7cff09c4e WHIRLPOOL c0caf66819920d35611b360feb47bfb4b85868e032f70566ec174e00880e04bad8f734cef5ffa0e3af805336a33393f8e7f05d39296e3b74adae698aa2fdc1cc
diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.ebuild
new file mode 100644
index 000000000..1005ecf88
--- /dev/null
+++ b/sci-biology/libgtextutils/libgtextutils-0.6.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Gordon Text utils Library"
+HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit/"
+SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.tar.bz2"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	emake install DESTDIR="${D}"
+}
diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml
new file mode 100644
index 000000000..07b525505
--- /dev/null
+++ b/sci-biology/libgtextutils/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>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>