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

[Martin Mokrejs]

commit:     7211dfa04b9f68a765a5a48c254b3ee380bcdcef
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 29 19:11:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 29 19:11:17 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7211dfa0

sci-biology/subread: new package

Package-Manager: portage-2.2.15

---
 sci-biology/subread/ChangeLog            |  9 +++++++
 sci-biology/subread/metadata.xml         |  9 +++++++
 sci-biology/subread/subread-1.4.6.ebuild | 40 ++++++++++++++++++++++++++++++++
 3 files changed, 58 insertions(+)

diff --git a/sci-biology/subread/ChangeLog b/sci-biology/subread/ChangeLog
new file mode 100644
index 0000000..df4d2f8
--- /dev/null
+++ b/sci-biology/subread/ChangeLog
@@ -0,0 +1,9 @@
+# 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@×××××××××××××××.cz> +metadata.xml,
+  +subread-1.4.6.ebuild:
+  sci-biology/subread: new package

diff --git a/sci-biology/subread/metadata.xml b/sci-biology/subread/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/subread/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@×××××××××××××××.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 0000000..2e1de79
--- /dev/null
+++ b/sci-biology/subread/subread-1.4.6.ebuild
@@ -0,0 +1,40 @@
+# 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
+}