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

[Martin Mokrejs]

commit:     bae149ca5806b0db04206b0569f733a6c41a1007
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Sep 24 11:24:04 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Sep 24 11:24:04 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bae149ca

sci-biology/idba: new package, needed by biopieces, github issue #381

Package-Manager: portage-2.3.0

 sci-biology/idba/idba-1.1.1.ebuild | 34 ++++++++++++++++++++++++++++++++++
 sci-biology/idba/idba-9999.ebuild  | 34 ++++++++++++++++++++++++++++++++++
 sci-biology/idba/metadata.xml      | 12 ++++++++++++
 3 files changed, 80 insertions(+)

diff --git a/sci-biology/idba/idba-1.1.1.ebuild b/sci-biology/idba/idba-1.1.1.ebuild
new file mode 100644
index 0000000..d3a82a5
--- /dev/null
+++ b/sci-biology/idba/idba-1.1.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers"
+HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba
+	https://code.google.com/archive/p/hku-idba"
+SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/hku-idba/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	# Makefile.am also forces '-fopenmp -pthread', do we care?
+	find . -name Makefile.in | while read f; do \
+		sed -e 's/-Wall -O3//' -i $f || die
+	done || die
+	default
+}
+
+src_install(){
+	default
+	# https://github.com/loneknightpy/idba/issues/23
+	rm "${D}"/usr/bin/scan.py "${D}"/usr/bin/run-unittest.py || die
+	rm bin/test bin/*.o bin/Makefile* || die # avoid file collision
+	dobin bin/*
+}

diff --git a/sci-biology/idba/idba-9999.ebuild b/sci-biology/idba/idba-9999.ebuild
new file mode 100644
index 0000000..3252524
--- /dev/null
+++ b/sci-biology/idba/idba-9999.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3
+
+DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers"
+HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud"
+EGIT_REPO_URI="https://github.com/loneknightpy/idba.git"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	find . -name Makefile.in | while read f; do \
+		sed -e 's/-Wall -O3//' -i $f || die
+	done
+	default
+}
+
+src_install(){
+	default
+	# https://github.com/loneknightpy/idba/issues/23
+	rm "${D}"/usr/bin/scan.py "${D}"/usr/bin/run-unittest.py || die
+	rm bin/test bin/*.o bin/Makefile* || die # avoid file collision
+	dobin bin/*
+}

diff --git a/sci-biology/idba/metadata.xml b/sci-biology/idba/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/idba/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>