commit: 0097320955e9522a3b7b082a9ec3aa803dae2a0e Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 22:36:38 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 22:36:38 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00973209
sci-biology/inGAP-bin: new package; needs java team help Package-Manager: portage-2.2.7 --- sci-biology/inGAP-bin/ChangeLog | 9 +++++++ sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild | 39 ++++++++++++++++++++++++++++ sci-biology/inGAP-bin/metadata.xml | 9 +++++++ 3 files changed, 57 insertions(+) diff --git a/sci-biology/inGAP-bin/ChangeLog b/sci-biology/inGAP-bin/ChangeLog new file mode 100644 index 0000000..c573f62 --- /dev/null +++ b/sci-biology/inGAP-bin/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/inGAP-bin +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*inGAP-bin-3.0.1 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + +inGAP-bin-3.0.1.ebuild, +metadata.xml: + sci-biology/inGAP-bin: new package; needs java team help diff --git a/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild new file mode 100644 index 0000000..0c7903c --- /dev/null +++ b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MY_PV="3_0_1" +S="${WORKDIR}"/inGAP_"${MY_PV}" + +DESCRIPTION="Detect SNPs and indels from Next-gen sequences using a Bayesian algorithm" +HOMEPAGE="http://sites.google.com/site/nextgengenomics/ingap + http://sourceforge.net/projects/ingap/"; +SRC_URI="http://sourceforge.net/projects/ingap/files/ingap/v"${PV}"/inGAP_"${MY_PV}".tgz"; + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-java/jfreechart + dev-java/swing-layout + dev-java/jcommon + dev-java/itext + dev-java/bytecode + dev-java/biojava + dev-java/absolutelayout" # gnujaxp ? + +src_install(){ + dobin inGAP.jar || die + # dobin external/bin/{primer3_core, run_cpp, trf} + mv manual.pdf inGAP_Manual.pdf || die + dodoc inGAP_Manual.pdf || die + insinto /usr/share/inGAP + doins doc/manual.htm + insinto /usr/share/inGAP/manual_files + doins doc/manual_files/*.png +} diff --git a/sci-biology/inGAP-bin/metadata.xml b/sci-biology/inGAP-bin/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/inGAP-bin/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>
