commit: a6c3140a2b483a8bb7fb63a914084e731d68cb39 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue May 5 14:00:42 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue May 5 14:00:42 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6c3140a
sci-biology/STAR: new package Package-Manager: portage-2.2.18 sci-biology/STAR/ChangeLog | 10 ++++++++++ sci-biology/STAR/STAR-2.4.1c.ebuild | 38 +++++++++++++++++++++++++++++++++++++ sci-biology/STAR/STAR-9999.ebuild | 37 ++++++++++++++++++++++++++++++++++++ sci-biology/STAR/metadata.xml | 9 +++++++++ 4 files changed, 94 insertions(+) diff --git a/sci-biology/STAR/ChangeLog b/sci-biology/STAR/ChangeLog new file mode 100644 index 0000000..b718477 --- /dev/null +++ b/sci-biology/STAR/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/STAR +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*STAR-2.4.1c (05 May 2015) +*STAR-9999 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +STAR-2.4.1c.ebuild, + +STAR-9999.ebuild, +metadata.xml: + sci-biology/STAR: new package diff --git a/sci-biology/STAR/STAR-2.4.1c.ebuild b/sci-biology/STAR/STAR-2.4.1c.ebuild new file mode 100644 index 0000000..bed7e73 --- /dev/null +++ b/sci-biology/STAR/STAR-2.4.1c.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" +HOMEPAGE="http://code.google.com/p/rna-star/"; +SRC_URI="https://github.com/alexdobin/STAR/archive/STAR_"${PV}".tar.gz"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# sci-biology/htslib +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/STAR-STAR_"${PV}" + +# contains bundled STAR-Fusion +src_prepare(){ + sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die + sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die +} + +src_compile(){ + cd source || die + emake STAR +} + +src_install(){ + dobin source/STAR + dodoc doc/STARmanual.pdf +} diff --git a/sci-biology/STAR/STAR-9999.ebuild b/sci-biology/STAR/STAR-9999.ebuild new file mode 100644 index 0000000..149226a --- /dev/null +++ b/sci-biology/STAR/STAR-9999.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" +HOMEPAGE="http://code.google.com/p/rna-star/"; +EGIT_REPO_URI="https://github.com/alexdobin/STAR.git"; +# http://rna-star.googlecode.com/files/STARmanual_2.3.0.1.pdf + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# contains bundled version sci-biology/htslib-0.0.1 +DEPEND="" +RDEPEND="${DEPEND}" + +# contains bundled STAR-Fusion +src_prepare(){ + sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die + sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die +} + +src_compile(){ + cd source || die + emake STAR +} + +src_install(){ + dobin source/STAR + dodoc doc/STARmanual.pdf +} diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/STAR/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>
