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 <[email protected]> +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>[email protected]</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" +}
