commit: 90b414bd2d7195138343e5ea4d129c3e6b067a6e Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jan 8 12:42:22 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jan 8 12:42:22 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=90b414bd
sci-biology/vague-bin: new java binary package Package-Manager: portage-2.2.7 --- sci-biology/vague-bin/ChangeLog | 9 ++++++ sci-biology/vague-bin/files/vague.patch | 8 ++++++ sci-biology/vague-bin/metadata.xml | 9 ++++++ sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 41 ++++++++++++++++++++++++++++ 4 files changed, 67 insertions(+) diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog new file mode 100644 index 0000000..30734b2 --- /dev/null +++ b/sci-biology/vague-bin/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/vague-bin +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*vague-bin-1.0.5 (08 Jan 2015) + + 08 Jan 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +files/vague.patch, + +metadata.xml, +vague-bin-1.0.5.ebuild: + sci-biology/vague-bin: new java binary package diff --git a/sci-biology/vague-bin/files/vague.patch b/sci-biology/vague-bin/files/vague.patch new file mode 100644 index 0000000..61f4c1a --- /dev/null +++ b/sci-biology/vague-bin/files/vague.patch @@ -0,0 +1,8 @@ +--- vague.ori 2015-01-08 13:31:31.755604378 +0100 ++++ vague 2015-01-08 13:31:49.525604424 +0100 +@@ -1,4 +1,4 @@ + echo "Starting Vague, please wait..." + export VAGUE_DIR=`dirname $0` + export PATH=$PATH:$VAGUE_DIR +-java -Xmx3750m -jar `dirname $0`/vague.jar $* ++java -Xmx3750m -jar /usr/share/vague-bin/lib/vague.jar $* diff --git a/sci-biology/vague-bin/metadata.xml b/sci-biology/vague-bin/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/vague-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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild new file mode 100644 index 0000000..479d88a --- /dev/null +++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="GUI for Velvet de novo assembler" +HOMEPAGE="http://www.vicbioinformatics.com/software.vague.shtml"; + +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague"; + KEYWORDS="" +else + SRC_URI="http://www.vicbioinformatics.com/vague-"${PV}".tar.gz"; + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=">=virtual/jre-1.5 + sci-biology/velvet + sci-biology/velvetk" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/vague-"${PV}" + +src_prepare(){ + epatch "${FILESDIR}"/vague.patch +} + +src_install(){ + dobin vague + java-pkg_dojar vague.jar || die +}
