commit: 6af4711acbcf79597c14aebf34705c51dec00108 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sun Mar 26 08:35:09 2017 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Mar 26 08:35:09 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6af4711a
Drop masked package - sci-biology/iCORN2 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/iCORN2/iCORN2-0.95.ebuild | 56 ----------------------------------- sci-biology/iCORN2/metadata.xml | 12 -------- 3 files changed, 69 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index d57ef61cf..29b07cf02 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,7 +36,6 @@ sci-mathematics/scilab # Justin Lecher <[email protected]> (24 April 2016) # rev dep missing keywords -sci-biology/iCORN2 # Justin Lecher <[email protected]> (9 Feb 2016) # rev dep masked diff --git a/sci-biology/iCORN2/iCORN2-0.95.ebuild b/sci-biology/iCORN2/iCORN2-0.95.ebuild deleted file mode 100644 index 50b96c893..000000000 --- a/sci-biology/iCORN2/iCORN2-0.95.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Iteratively map reads to a reference, fix mismatches and indels with GATK/picard" -HOMEPAGE="http://icorn.sourceforge.net/ - http://sourceforge.net/projects/icorn"; -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/ICORN2/icorn2.V${PV}.tgz - http://icorn.sourceforge.net/manual.html -> ${PN}_manual.html" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=" - sci-biology/snpomatic - || ( sci-biology/smalt sci-biology/smalt-bin ) - sci-biology/samtools:= - sci-biology/gatk - sci-biology/picard" -RDEPEND="${DEPEND} - dev-lang/perl - app-shells/tcsh" - -S="${WORKDIR}"/ICORN2 - -src_unpack(){ - default - # The bundled files GenomeAnalysisTK.jar from GATK - # contains bundled MarkDuplicates.jar from picard - # both .jar files were supposed to be in $ICORN2_HOME - rm -f *~ smalt || die -} - -src_prepare(){ - sed -e "s#java -jar \$ICORN2_HOME#java -jar /usr/share/${PN}/lib#" -i *.sh || die -} - -# the tarball is a terrible mess -src_install(){ - dobin *.pl *.sh - insinto /usr/share/"${PN}"/lib - doins GenomeAnalysisTK.jar MarkDuplicates.jar - insinto /usr/share/"${PN}"/LSF - doins LSF/* - dodoc README.txt - newdoc "${DISTDIR}"/"${PN}"_manual.html manual.html -} - -# http://icorn.sourceforge.net/documentation.html -# Define the shell variable ICORN_HOME, PILEUP_HOME and SNPOMATIC_HOME -pkg_postinst(){ - einfo "Ideally install Artemis ACT viewer or gap4 from staden package" -} diff --git a/sci-biology/iCORN2/metadata.xml b/sci-biology/iCORN2/metadata.xml deleted file mode 100644 index f68a1b6fa..000000000 --- a/sci-biology/iCORN2/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?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>
