commit: a7bf4e9d7d31c5c27213f618b1160b0d7006ac1c Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 18:15:12 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 18:15:12 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7bf4e9d
sci-biology/bambino: a new package, maybe should have -bin in its name?; needs decent inspection from java team for sure Package-Manager: portage-2.2.7 --- sci-biology/bambino/ChangeLog | 11 ++++++++++ sci-biology/bambino/bambino-1.02.ebuild | 36 +++++++++++++++++++++++++++++++++ sci-biology/bambino/bambino-1.06.ebuild | 36 +++++++++++++++++++++++++++++++++ sci-biology/bambino/metadata.xml | 9 +++++++++ 4 files changed, 92 insertions(+) diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog new file mode 100644 index 0000000..1cc049f --- /dev/null +++ b/sci-biology/bambino/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/bambino +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*bambino-1.02 (23 Mar 2014) +*bambino-1.06 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + +bambino-1.02.ebuild, +bambino-1.06.ebuild, +metadata.xml: + sci-biology/bambino: a new package, maybe should have -bin in its name?; needs + decent inspection from java team for sure diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild new file mode 100644 index 0000000..4ea6c9d --- /dev/null +++ b/sci-biology/bambino/bambino-1.02.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit java-pkg-2 eutils + +DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files" +HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"; + +# bug #377305 +SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar + https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.02.jar" + +LICENSE="bambino" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=virtual/jdk-1.6 + sci-biology/picard + dev-java/jdbc-mysql" + +src_install(){ + insinto "${DESTDIR}"/usr/share/"${PN}"/lib + doins "${DISTDIR}"/bambino_core_"${PV}".jar || die + doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die + + einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'" + einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'" + einfo "More info at "${HOMEPAGE} + +} diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild new file mode 100644 index 0000000..864beee --- /dev/null +++ b/sci-biology/bambino/bambino-1.06.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit java-pkg-2 eutils + +DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files" +HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"; + +# bug #377305 +SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar + https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.06.jar" + +LICENSE="bambino" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=virtual/jdk-1.6 + sci-biology/picard + dev-java/jdbc-mysql" + +src_install(){ + insinto "${DESTDIR}"/usr/share/"${PN}"/lib + doins "${DISTDIR}"/bambino_core_"${PV}".jar || die + doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die + + einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'" + einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'" + einfo "More info at "${HOMEPAGE} + +} diff --git a/sci-biology/bambino/metadata.xml b/sci-biology/bambino/metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/bambino/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>
