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

[Martin Mokrejs]

commit:     9ce7d7d02ffa5ea884d926a61506108d5db723a5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:14:56 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:14:56 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ce7d7d0

sci-biology/sga: new package; forces its own optimization flags but works fine

---
 sci-biology/sga/ChangeLog       | 10 +++++++++
 sci-biology/sga/metadata.xml    |  9 ++++++++
 sci-biology/sga/sga-9999.ebuild | 47 +++++++++++++++++++++++++++++++++++++++++
 3 files changed, 66 insertions(+)

diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog
new file mode 100644
index 0000000..0f7e181
--- /dev/null
+++ b/sci-biology/sga/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/sga
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*sga-9999 (24 Mar 2014)
+
+  24 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +sga-9999.ebuild,
+  +metadata.xml:
+  new package; forces its own optimization flags but works fine
+

diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/sga/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/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
new file mode 100644
index 0000000..5393f87
--- /dev/null
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="String Graph Assembler for short-read assemblies"
+HOMEPAGE="https://github.com/jts/sga"
+EGIT_REPO_URI="git://github.com/jts/sga"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE="jemalloc python"
+
+DEPEND="dev-cpp/sparsehash
+	sci-biology/bamtools
+	sys-libs/zlib
+	jemalloc? ( dev-libs/jemalloc )
+	python? ( sci-biology/pysam
+			sci-biology/ruffus )"
+RDEPEND="${DEPEND}"
+
+src_configure(){
+	cd src || die
+	./autogen.sh
+	econf --with-bamtools=/usr
+}
+
+src_compile(){
+	cd src || die
+	emake
+}
+
+src_install(){
+	cd src || die
+	dodoc README
+	emake install DESTDIR="${D}"
+	insinto /usr/share/sga/examples
+	doins examples/*
+	cd .. ||
+	dodoc README.md
+}