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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-20 23:21:41 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-20 23:21:41 +0100 |
| commit | 80a18f092e75c49d6cd4dae6a460c197988095b7 (patch) | |
| tree | d5d39b555bb60f542f5e8dd48b448b4a0e84611e | |
| parent | Merge branch 'master' of ssh://github.com/gentoo-science/sci (diff) | |
| download | sci-80a18f092e75c49d6cd4dae6a460c197988095b7.tar.gz sci-80a18f092e75c49d6cd4dae6a460c197988095b7.tar.bz2 sci-80a18f092e75c49d6cd4dae6a460c197988095b7.zip | |
sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 version or whichever
Package-Manager: portage-2.2.15
| -rw-r--r-- | sci-biology/angsd/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/angsd/angsd-9999.ebuild | 49 | ||||
| -rw-r--r-- | sci-biology/angsd/metadata.xml | 9 |
3 files changed, 68 insertions, 0 deletions
diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog new file mode 100644 index 000000000..a0ed7633e --- /dev/null +++ b/sci-biology/angsd/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/angsd +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*angsd-9999 (20 Mar 2015) + + 20 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +angsd-9999.ebuild, + +metadata.xml: + sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 + version or whichever diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild new file mode 100644 index 000000000..2850ddc45 --- /dev/null +++ b/sci-biology/angsd/angsd-9999.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="Population genetics analysis package" +HOMEPAGE="http://www.popgen.dk/angsd" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/ANGSD/angsd.git" + KEYWORDS="" +else + EGIT_REPO_URI="https://github.com/ANGSD/angsd.git" + EGIT_BRANCH="0.700" + KEYWORDS="" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="" + +DEPEND="dev-lang/R + sci-libs/htslib" +RDEPEND="${DEPEND}" + +# https://github.com/ANGSD/angsd/issues/9 +src_prepare(){ + sed -e 's@FLAGS=-O3@FLAGS=@' \ + -e 's@HTSLIB = .*@HTSLIB = -lhts@' \ + -e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die + sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \ + -e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die + sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die +} + +src_compile(){ + emake HTS=/usr/include +} + +src_install(){ + dobin angsd + dodoc README.md + cd misc || die + dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix +} diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/angsd/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> |