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

[Martin Mokrejs]

commit:     bf1b944dd35395338a376aab9eb3cb7bc29fb24a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 11:05:31 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 11:05:31 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf1b944d

sci-biology/stampy-bin: working ebuild thanks to soap <AT> g.o

Package-Manager: portage-2.3.0

 sci-biology/stampy-bin/metadata.xml             | 12 +++++++
 sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild | 43 +++++++++++++++++++++++++
 2 files changed, 55 insertions(+)

diff --git a/sci-biology/stampy-bin/metadata.xml b/sci-biology/stampy-bin/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/stampy-bin/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@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild b/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild
new file mode 100644
index 0000000..0f46696
--- /dev/null
+++ b/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 )
+
+inherit toolchain-funcs python-r1 python-utils-r1
+
+DESCRIPTION="Map highly divergent short reads to a reference"
+HOMEPAGE="http://www.well.ox.ac.uk/project-stampy"
+SRC_URI="stampy-${PV}.tar.gz"
+
+LICENSE="stampy-academic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/stampy-${PV}
+
+# FIXME: the makefile calls python but fails if that is under python-3.4, 2.7 works
+# FIXME: respect CC and CXX
+
+src_prepare(){
+	sed -e 's/-O2 -Wall/$(CFLAGS)/' -i makefile || die
+}
+
+src_install(){
+	dobin *.py
+	python_foreach_impl python_domodule maptools.so
+	python_moduleinto Stampy
+	python_foreach_impl python_domodule build/python2.7/Stampy/*.pyc # only *.pyc files available
+	python_moduleinto ext
+	python_foreach_impl python_domodule build/python2.7/ext/*.pyc # only *.pyc files available
+	python_moduleinto plugins
+	python_foreach_impl python_domodule build/python2.7/plugins/*.py*
+	dodoc README.txt
+}