commit: 1bc9bf063980829008293505ed8468e6495b3113 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Aug 1 16:32:12 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Aug 1 16:32:12 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1bc9bf06
sci-biology/plink: version bump (non-maintainer) Package-Manager: portage-2.3.0 sci-biology/plink/metadata.xml | 16 ++++++++ sci-biology/plink/plink-1.90_pre160731.ebuild | 55 +++++++++++++++++++++++++++ 2 files changed, 71 insertions(+) diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml new file mode 100644 index 0000000..c281934 --- /dev/null +++ b/sci-biology/plink/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="webcheck"> + add support for online update checking every time the program starts + </flag> + <flag name="R"> + add support R language + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild new file mode 100644 index 0000000..1048be0 --- /dev/null +++ b/sci-biology/plink/plink-1.90_pre160731.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Whole genome association analysis toolset" +HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"; +SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + app-arch/unzip + virtual/pkgconfig" +RDEPEND=" + sys-libs/zlib + virtual/cblas + virtual/lapack + " + +S="${WORKDIR}/" + +# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. +# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. + +src_prepare() { + sed \ + -e 's:zlib-1.2.8/zlib.h:zlib.h:g' \ + -i *.{c,h} || die + + sed \ + -e 's:g++:$(CXX):g' \ + -e 's:gcc:$(CC):g' \ + -e 's:gfortran:$(FC):g' \ + -i Makefile || die + tc-export PKG_CONFIG +} + +src_compile() { + emake \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \ + BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)" +} + +src_install() { + newbin plink p-link +}
