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

[Nicolas Bock]

commit:     1f2d059a9dabfde3feba094757e22afdb4ee2567
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:03:36 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:27:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1f2d059a

sci-biology/stacks: skeleton for a new package; needs webapp team help, *some* Makefile's need proper DESTDIR support

Package-Manager: portage-2.2.7

---
 sci-biology/stacks/ChangeLog          | 10 +++++++
 sci-biology/stacks/metadata.xml       |  9 +++++++
 sci-biology/stacks/stacks-1.16.ebuild | 49 +++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
new file mode 100644
index 0000000..ea6c94c
--- /dev/null
+++ b/sci-biology/stacks/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/stacks
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*stacks-1.16 (28 Mar 2014)
+
+  28 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +metadata.xml,
+  +stacks-1.16.ebuild:
+  sci-biology/stacks: skeleton for a new package; needs webapp team help, *some*
+  Makefile's need proper DESTDIR support

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

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
new file mode 100644
index 0000000..f55dd68
--- /dev/null
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit flag-o-matic eutils perl-module webapp
+
+DESCRIPTION="Analyze Restriction enzyme-based data, draw genetic maps, population genomics (RAD-seq Illumina sequencing)"
+HOMEPAGE="http://creskolab.uoregon.edu/stacks"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz"
+
+LICENSE="GPL-3"
+# SLOT="0" # webapp ebuilds do not set SLOT
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+	dev-cpp/sparsehash
+	sci-biology/samtools
+	sci-biology/bamtools"
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	>=dev-lang/php-5
+	dev-perl/DBD-mysql"
+
+src_configure() {
+	econf --enable-bam --enable-sparsehash
+	webapp_src_preinst
+	sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
+}
+
+src_compile(){
+	emake DESTDIR="${D}"
+}
+
+src_install() {
+	emake install DESTDIR="${D}"
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install DESTDIR="${D}"
+	webapp_src_install || die "Failed running webapp_src_install"
+}
+
+
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}