commit: 80a18f092e75c49d6cd4dae6a460c197988095b7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 20 22:21:41 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 20 22:21:41 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=80a18f09
sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 version or whichever Package-Manager: portage-2.2.15 sci-biology/angsd/ChangeLog | 10 ++++++++ sci-biology/angsd/angsd-9999.ebuild | 49 +++++++++++++++++++++++++++++++++++++ sci-biology/angsd/metadata.xml | 9 +++++++ 3 files changed, 68 insertions(+) diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog new file mode 100644 index 0000000..a0ed763 --- /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 <mmokr...@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 0000000..2850ddc --- /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 0000000..2bc8930 --- /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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
