[gentoo-commits] proj/sci:master commit in: sci-biology/plink/

[Martin Mokrejs]

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-biology@g.o</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
+}