commit: a81192976249025c253af5645ce2510992f899a9 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 10 20:20:53 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 10 20:20:53 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a8119297
sci-biology/somatic-sniper: new package Package-Manager: portage-2.2.28 sci-biology/somatic-sniper/metadata.xml | 12 +++++++++ .../somatic-sniper/somatic-sniper-1.0.4.ebuild | 29 ++++++++++++++++++++++ 2 files changed, 41 insertions(+) diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/somatic-sniper/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild new file mode 100644 index 0000000..e4629b6 --- /dev/null +++ b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs" +HOMEPAGE="http://gmt.genome.wustl.edu"; +SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz" +# git clone git://github.com/genome/somatic-sniper.git + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sys-libs/zlib + sys-libs/ncurses:* + sci-biology/samtools:0.1-legacy" +RDEPEND="${DEPEND}" + +# contains bundled copy of samtools-0.1.6 but links using a static version +# cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1 +# /usr/bin/x86_64-pc-linux-gnu-gcc -Wall -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz + +# contains build-common from git tree
