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

[Martin Mokrejs]

commit:     c0c2589594db6900b277d68628ece4d62254e1ae
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 20:22:23 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 20:22:23 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c0c25895

sci-biology/arachne: new package; does not compile (upstream contacted) and the LICENSE is not exactly MIT?

Package-Manager: portage-2.2.28

 sci-biology/arachne/arachne-46233.ebuild | 41 ++++++++++++++++++++++++++++++++
 sci-biology/arachne/metadata.xml         | 12 ++++++++++
 2 files changed, 53 insertions(+)

diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
new file mode 100644
index 0000000..71fc0b8
--- /dev/null
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)"
+HOMEPAGE="https://www.broadinstitute.org/crd/wiki
+	http://genome.cshlp.org/content/12/1/177.abstract"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
+SLOT="0"
+KEYWORDS=""
+IUSE="doc openmp"
+
+DEPEND="dev-libs/xerces-c
+	doc? ( virtual/latex-base app-text/dvipsk )"
+RDEPEND="${DEPEND}"
+
+# needs >=g++-4.7 but does not compile with 5.3.0
+
+# --disable-openmp to disable requirement for OpenMP-capable compiler
+src_configure() {
+	local myconf=()
+	use openmp || myconf+=( --disable-openmp )
+	econf ${myconf[@]}
+}
+
+# set the following environment variables
+# http://www.broadinstitute.org/crd/wiki/index.php/Setup
+# 
+# ARACHNE_PRE
+# ARACHNE_BIN_DIR
+# ARACHNE_PRETTY_HELP 
+
+pkg_postinst(){
+	einfo "Please add these to your ~/.bashrc"
+	einfo "limit stacksize 100000"
+	einfo "limit datasize unlimited"
+}

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