commit: 43383a65794cbfd08269dbaea69a67d7787479d8 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jan 22 21:45:58 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jan 22 21:45:58 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43383a65
sci-biology/trimmomatic: new package Package-Manager: portage-2.2.15 --- sci-biology/trimmomatic/ChangeLog | 9 +++++++ sci-biology/trimmomatic/metadata.xml | 9 +++++++ sci-biology/trimmomatic/trimmomatic-0.32.ebuild | 36 +++++++++++++++++++++++++ 3 files changed, 54 insertions(+) diff --git a/sci-biology/trimmomatic/ChangeLog b/sci-biology/trimmomatic/ChangeLog new file mode 100644 index 0000000..119ca3f --- /dev/null +++ b/sci-biology/trimmomatic/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/trimmomatic +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*trimmomatic-0.32 (22 Jan 2015) + + 22 Jan 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +metadata.xml, + +trimmomatic-0.32.ebuild: + sci-biology/trimmomatic: new package diff --git a/sci-biology/trimmomatic/metadata.xml b/sci-biology/trimmomatic/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/trimmomatic/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/trimmomatic/trimmomatic-0.32.ebuild b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild new file mode 100644 index 0000000..662ceea --- /dev/null +++ b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Illumina adapter trimming tool" +HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"; +SRC_URI="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip + http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf" + +# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=">=virtual/jdk-1.6 + dev-java/ant-core" +RDEPEND="${DEPEND} + >=virtual/jre-1.6" + +# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works + +EANT_BUILD_TARGET="dist" + +src_install() { + java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar" + insinto /usr/share/"${PN}"/Illumina + doins adapters/*.fa + insinto /usr/share/doc/"${P}" + dodoc "${DISTDIR}"/"${P}"_manual.pdf +}
