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

4 files changed, 69 insertions, 0 deletions

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
new file mode 100644
index 000000000..ea6c94cd7
--- /dev/null
+++ b/sci-biology/stacks/ChangeLog
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+# 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@fold.natur.cuni.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/Manifest b/sci-biology/stacks/Manifest
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index 000000000..88457444f
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+++ b/sci-biology/stacks/Manifest
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+DIST stacks-1.16.tar.gz 408947 SHA256 ac6eb7db461cf42e72106e707998562400885919b74290b995def39ac87ac203 SHA512 0c80d6db9cc9d2b1a02bb31f25f8a20845ac1113bc3ae7cf87067e997ee0ff58728c7ac5cdadb435ebc9d01b92ed4dfe8399b549a470e794353a4e84008f8d5f WHIRLPOOL 4c53928c28b9567daa452f9b21ffc9d52593adfdb7e99bf3245b4be5ce3fd65d530c9e772d61b7797f395581d97df3d9556a8844b96ca09e80413eca6d646260
diff --git a/sci-biology/stacks/metadata.xml b/sci-biology/stacks/metadata.xml
new file mode 100644
index 000000000..2bc893037
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+++ b/sci-biology/stacks/metadata.xml
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+<?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@fold.natur.cuni.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 000000000..f55dd6815
--- /dev/null
+++ b/sci-biology/stacks/stacks-1.16.ebuild
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+# 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"
+}