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

[Martin Mokrejs]

commit:     a788b3a56fa7e60683c10ae8c8e73490d1575e0f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 20:52:30 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 20:52:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a788b3a5

sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak to get all configure's running

---
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild | 63 ++++++++++++++++++++++++++++++++
 sci-biology/MaSuRCA/metadata.xml         |  9 +++++
 2 files changed, 72 insertions(+)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
new file mode 100644
index 0000000..28934c3
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
+		ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+		app-arch/bzip2"
+RDEPEND="${DEPEND}"
+
+# the ebuild mimics "${S}"/install.sh
+src_configure(){
+	cd jellyfish-1.1.11 || die
+	econf
+
+	cd ../jellyfish-2.0.0rc1 || die
+	econf --program-suffix=-2.0
+
+	cd ../CA/kmer || die
+	sh ./configure.sh
+	econf
+
+	cd ../../SuperReads-0.3.2 || die
+	econf
+
+	cd ../quorum-0.3.2 || die
+	econf --enable-relative-paths --with-relative-jf-path
+}
+
+src_compile(){
+	cd jellyfish-1.1.11 || die
+	emake
+
+	cd ../jellyfish-2.0.0rc1 || die
+	emake
+
+	cd ../CA/kmer || die
+	emake
+
+	cd ../../CA/src || die
+	emake
+
+	cd ../SuperReads-0.3.2 || die
+	emake
+
+	cd ../quorum-0.3.2 || die
+	emake
+}
+
+src_install(){
+	dobin masurca
+	dodoc sr_config_example.txt
+}

diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/MaSuRCA/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>