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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-24 14:57:44 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-24 14:57:44 +0100 |
| commit | 57aaac2250383519cf73bc1d9d3fc20a1a3c8240 (patch) | |
| tree | e4250f735035ff1d229314bd0cf9e328b952f753 /sci-biology | |
| parent | sci-biology/genepop: version bump, install PDF doc (diff) | |
| download | sci-57aaac2250383519cf73bc1d9d3fc20a1a3c8240.tar.gz sci-57aaac2250383519cf73bc1d9d3fc20a1a3c8240.tar.bz2 sci-57aaac2250383519cf73bc1d9d3fc20a1a3c8240.zip | |
sci-biology/verifyBamID: new package, would benefit unbundling of libStatGen
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/verifyBamID/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/verifyBamID/metadata.xml | 12 | ||||
| -rw-r--r-- | sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild | 39 |
3 files changed, 53 insertions, 0 deletions
diff --git a/sci-biology/verifyBamID/Manifest b/sci-biology/verifyBamID/Manifest new file mode 100644 index 000000000..a6034694d --- /dev/null +++ b/sci-biology/verifyBamID/Manifest @@ -0,0 +1,2 @@ +DIST libStatGen-1.0.13.tar.gz 558682 SHA256 a67a3126fbf227a5c3a4de044447bf01eb8e091c737f7696449f764e42926339 SHA512 bcce3dd2f343e5941857d5bca0f2960d69b3e1083da6312e018a96bb92fb8dbc91ac511e062b024720c45508aa805d3f4f6511f60201438176a898ab789e746f WHIRLPOOL 533f255adc73d5aff0c45191d97a138723ff4a84e70f72bc0f66430b62071afe7ff6efa09d519ebce9954263b5c5a1a8ce066d648305aa2602a0d831abbdb6f6 +DIST verifyBamID-1.1.3.tar.gz 68447 SHA256 985584895e31b40422745d60542e5a30a3038ca735c65a8ba7802da58d721e22 SHA512 1b39b1f7b8a40f3c6c08af5a4ad24b8aebe5dc0dc3b1bf4401632fa6cac56dc8d5e17c18f142caa5cc00c7c654f43737b2550149f4c4416166f439688634235e WHIRLPOOL 97a3d0f3fcb0388d016b5406921eb63f3cd6585b827c0c7dbc0226325c77a113b7eb142fc0d2c1f6fe6535419c56e51946ffe9ff0c3b2f35e1e0ab7f70568f69 diff --git a/sci-biology/verifyBamID/metadata.xml b/sci-biology/verifyBamID/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/verifyBamID/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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild new file mode 100644 index 000000000..dfea2c485 --- /dev/null +++ b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Verify sample identity/mix and genotype concordance" +HOMEPAGE="http://genome.sph.umich.edu/wiki/VerifyBamID" +SRC_URI="https://github.com/statgen/verifyBamID/archive/v1.1.3.tar.gz -> ${P}.tar.gz + https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz -> libStatGen-1.0.13.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# DEPEND="sci-libs/libStatGen" # TODO: currently it uses its own bundled copy +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + # unpack ./libStatGen-1.0.13/ contents + gzip -dc "${DISTDIR}"/libStatGen-1.0.13.tar.gz | tar xf - || die + ln -s libStatGen-1.0.13 libStatGen || die + cd "${WORKDIR}" || die + ln -s libStatGen-1.0.13 libStatGen || die +} + +src_compile(){ + # LIB_PATH_GENERAL="${EPREFIX}"/usr/"$(get_libdir)" emake + LIB_PATH_GENERAL="../libStatGen-1.0.13" emake +} + +src_install(){ + dobin bin/verifyBamID +} |