commit: e4f568402bfead6e32904c59ce41578b7617b851 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Jan 20 21:35:57 2018 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sat Jan 20 21:35:57 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4f56840
sci-biology/pilon-bin: new, albeit binary package The sources are in scala language, btw. Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/pilon-bin/metadata.xml | 12 ++++++++++++ sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 30 +++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/pilon-bin/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild new file mode 100644 index 000000000..2284e6418 --- /dev/null +++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit java-pkg-2 + +DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs" +HOMEPAGE="https://github.com/broadinstitute/pilon + https://github.com/broadinstitute/pilon/wiki"; +SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-java/sbt + >=virtual/jdk-1.5:*" +RDEPEND="${DEPEND} + >=virtual/jre-1.5:* + >=dev-java/htsjdk-1.130" + +S="${WORKDIR}" + +src_install(){ + cp -p "${DISTDIR}"/pilon-${PV}.jar . || die + java-pkg_dojar pilon-${PV}.jar +}
