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

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

[Martin Mokrejs]

commit:     fdadb1aefebd39ecb3836948d4008deba80cb903
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:35:37 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:35:37 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdadb1ae

sci-biology/perga: added some LICENSE, fix CFLAGS

Package-Manager: portage-2.2.28

 sci-biology/perga/metadata.xml      | 12 ++++++++++++
 sci-biology/perga/perga-9999.ebuild | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/perga/metadata.xml b/sci-biology/perga/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/perga/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/perga/perga-9999.ebuild b/sci-biology/perga/perga-9999.ebuild
new file mode 100644
index 0000000..4f79d72
--- /dev/null
+++ b/sci-biology/perga/perga-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit git-r3 eutils toolchain-funcs
+
+DESCRIPTION="Paired End Reads Guided Assembler"
+HOMEPAGE="https://github.com/hitbio/PERGA
+	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252104"
+EGIT_REPO_URI="https://github.com/hitbio/PERGA.git"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s/gcc -g /$(tc-getCC) ${CFLAGS} ${LDFLAGS} /" -i src/Makefile || die
+	sed -e 's/-Wl,-O1//' -i src/Makefile || die
+}
+
+# does not compile with gcc-5.3.0 but 4.9.3 works
+src_compile(){
+	cd src || die
+	emake
+}
+
+src_install(){
+	dobin src/perga
+	dodoc README
+}