[gentoo-commits] proj/sci:master commit in: sci-biology/consed2gap/

[Martin Mokrejs]

commit:     f650ffd23911ac46a4d47d3a641200ec2df67a67
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 22:42:41 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 22:42:41 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f650ffd2

sci-biology/consed2gap: new package, works

Package-Manager: portage-2.2.7

---
 sci-biology/consed2gap/ChangeLog                  |  9 ++++++
 sci-biology/consed2gap/consed2gap-20050520.ebuild | 38 +++++++++++++++++++++++
 sci-biology/consed2gap/metadata.xml               |  9 ++++++
 3 files changed, 56 insertions(+)

diff --git a/sci-biology/consed2gap/ChangeLog b/sci-biology/consed2gap/ChangeLog
new file mode 100644
index 0000000..ee91ed4
--- /dev/null
+++ b/sci-biology/consed2gap/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/consed2gap
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*consed2gap-20050520 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +consed2gap-20050520.ebuild, +metadata.xml:
+  sci-biology/consed2gap: new package, works

diff --git a/sci-biology/consed2gap/consed2gap-20050520.ebuild b/sci-biology/consed2gap/consed2gap-20050520.ebuild
new file mode 100644
index 0000000..9a0223f
--- /dev/null
+++ b/sci-biology/consed2gap/consed2gap-20050520.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+inherit perl-module perl-app
+
+DESCRIPTION="convert whole CONSED dataset to a GAP4 project"
+HOMEPAGE="http://genome.imb-jena.de/software/consed2gap/"
+SRC_URI="http://genome.imb-jena.de/software/consed2gap/consed2gap.tgz"
+
+LICENSE="FLI-Jena"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+		dev-lang/perl
+		sci-libs/io_lib
+		sci-biology/caftools
+		sci-biology/align_to_scf"
+
+MY_P="consed2gap"
+S="${WORKDIR}/${MY_P}"
+
+src_prepare(){
+	sed -i 's#/usr/local/bin/perl#/usr/bin/env perl#' bin/phrap2caf || die
+	sed -i 's#/usr/local/bin/perl#/usr/bin/env perl#' bin/badgerGetOpt.pl || die
+}
+
+src_install(){
+	dobin bin/consed2gap bin/phrap2caf bin/badgerGetOpt.pl || die
+	mkdir -p "${D}"/usr/share/"${PN}" || die
+	cp -r example "${D}"/usr/share/"${PN}" || die
+
+	cd bin && perl-module_src_install
+}

diff --git a/sci-biology/consed2gap/metadata.xml b/sci-biology/consed2gap/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/consed2gap/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>