commit: f140979d8539071c3643839bab3bd3736b42cfd5 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Apr 18 01:01:20 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Apr 18 01:01:20 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f140979d
sci-biology/cortex_var: new package with bundled htslib and gsl libraries Package-Manager: portage-2.2.18 sci-biology/cortex_var/ChangeLog | 9 +++++ sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 47 +++++++++++++++++++++++ sci-biology/cortex_var/metadata.xml | 9 +++++ 3 files changed, 65 insertions(+) diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog new file mode 100644 index 0000000..7be9c85 --- /dev/null +++ b/sci-biology/cortex_var/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/cortex_var +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cortex_var-1.0.5.21 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + +cortex_var-1.0.5.21.ebuild, +metadata.xml: + sci-biology/cortex_var: new package with bundled htslib and gsl libraries diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild new file mode 100644 index 0000000..391b45f --- /dev/null +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)" +HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"; +SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz + http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://www.well.ox.ac.uk/project-stampy + +DEPEND="sci-biology/vcftools + sci-libs/gsl + sci-libs/htslib + dev-lang/perl" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/CORTEX_release_v1.0.5.21 + +src_prepare(){ + sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die +} + +src_compile(){ + rm -rf libs/htslib libs/gsl-1.15 + make NUM_COLS=1 MAXK=31 cortex_var || die +} + +src_install(){ + bash install.sh || die + perl_set_version + insinto ${VENDOR_LIB} + doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* + echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + dodoc ${DISTDIR}/cortex_var_user_manual.pdf +} diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/cortex_var/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
