sci-biology/subread: new package

Package-Manager: portage-2.2.15

4 files changed, 59 insertions, 0 deletions

diff --git a/sci-biology/subread/ChangeLog b/sci-biology/subread/ChangeLog
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+++ b/sci-biology/subread/ChangeLog
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+# ChangeLog for sci-biology/subread
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*subread-1.4.6 (29 Jan 2015)
+
+  29 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +subread-1.4.6.ebuild:
+  sci-biology/subread: new package
diff --git a/sci-biology/subread/Manifest b/sci-biology/subread/Manifest
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+++ b/sci-biology/subread/Manifest
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+DIST subread-1.4.6-source.tar.gz 20173034 SHA256 930c1cb7e22236556e6f42499871a9bd11caa59b42da241e719f28a993afe508 SHA512 48636244d814ac985ba7ca2d1e54882b59c47145392958faab5680104ec2b35c7106d6351dfac675bfb5c5b8372e43585c603f76d830e3ddb25b6747a28b0132 WHIRLPOOL e7e684077de905fded06510787ce0f26c8e61a958ac01964c48d1cd67f47723300d237f0fd98f6ccd5930ebf8d47e050c09a06fd8e75b99686854db288b8f7b6
diff --git a/sci-biology/subread/metadata.xml b/sci-biology/subread/metadata.xml
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+++ b/sci-biology/subread/metadata.xml
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+<?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>
diff --git a/sci-biology/subread/subread-1.4.6.ebuild b/sci-biology/subread/subread-1.4.6.ebuild
new file mode 100644
index 000000000..2e1de7981
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+++ b/sci-biology/subread/subread-1.4.6.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="NGS suite for read mapping, analysis of mapped reads, summary of exon/intron/gene counts"
+HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/"
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="https://subread.svn.sourceforge.net/svnroot/subread/trunk"
+	#KEYWORDS="~amd64 ~x86"
+else
+	SRC_URI="http://sourceforge.net/projects/subread/files/"${P}"/"${P}"-source.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${S}"-source
+
+src_prepare(){
+	sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die
+}
+
+src_compile(){
+	cd src || die
+	emake -f Makefile.Linux
+}
+
+src_install(){
+	dobin bin/[a-s]* bin/utilities/*
+	dodoc README.txt doc/SubreadUsersGuide.pdf
+}