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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     f1305f2410140aee98085c7448eae116695a4b04
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 10 01:20:02 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 10 01:20:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1305f24

new package; install *.pm into PERL5LIB/cegma and pass that via env.d

---
 sci-biology/cegma/ChangeLog        |  8 ++++++++
 sci-biology/cegma/cegma-2.5.ebuild | 36 ++++++++++++++++++++++++++++++++++++
 sci-biology/cegma/metadata.xml     |  9 +++++++++
 3 files changed, 53 insertions(+)

diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog
new file mode 100644
index 0000000..8e87015
--- /dev/null
+++ b/sci-biology/cegma/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/cegma
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild,
+  +metadata.xml:
+  new package; install *.pm into PERL5LIB/cegma and pass that via env.d
+

diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild
new file mode 100644
index 0000000..ef8dfe5
--- /dev/null
+++ b/sci-biology/cegma/cegma-2.5.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Use set of 458 core proteins to predict genes in a genome and use them for training to find all genes"
+HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma"
+SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v"${PV}".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/perl
+	sci-biology/wise
+	>=sci-biology/hmmer-3.0
+	sci-biology/geneid
+	sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/CEGMA_v${PV}
+
+src_install(){
+	dobin bin/*
+	eval `perl '-V:installvendorlib'`
+	vendor_lib_install_dir="${installvendorlib}"
+	dodir ${vendor_lib_install_dir}/cegma
+	insinto ${vendor_lib_install_dir}/cegma
+	doins lib/*.pm
+
+	echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma"
+	# echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma"
+	doenvd ${S}"/99cegma" || die
+}

diff --git a/sci-biology/cegma/metadata.xml b/sci-biology/cegma/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cegma/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@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>