commit: 92cb6e9daf7c9865bfc003d4968b56501d5d00c6 Author: Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr> AuthorDate: Tue May 4 21:57:13 2021 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Tue May 4 22:29:36 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92cb6e9d
sci-biology/gatk: Remove last-rited pkg Closes: https://bugs.gentoo.org/780396 Closes: https://bugs.gentoo.org/574632 Closes: https://bugs.gentoo.org/542940 Closes: https://bugs.gentoo.org/515816 Closes: https://bugs.gentoo.org/431644 Closes: https://bugs.gentoo.org/418625 Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr> Closes: https://github.com/gentoo/gentoo/pull/20667 Signed-off-by: Sam James <sam <AT> gentoo.org> profiles/package.mask | 6 ------ sci-biology/gatk/Manifest | 1 - sci-biology/gatk/gatk-2.4.ebuild | 32 -------------------------------- sci-biology/gatk/metadata.xml | 11 ----------- 4 files changed, 50 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 34796fa37a1..e8d3aa29191 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -631,12 +631,6 @@ dev-java/slf4j-ext # Masked for removal in 30 days. dev-php/PEAR-Net_LDAP3 -# David Seifert <s...@gentoo.org> (2021-04-05) -# Completely broken, unmaintained, does not build. Newer version -# use Maven, good luck with that. Bugs #418625, #431644, #515816 -# #542940, #574632, #780396, removal in 30 days. -sci-biology/gatk - # Michał Górny <mgo...@gentoo.org> (2021-03-31) # New versions remove PORTAGE_CONFIGROOT support, breaking a lot # of scripts. diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest deleted file mode 100644 index 58798a939a0..00000000000 --- a/sci-biology/gatk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gatk-2.4.tar.gz 9106774 BLAKE2B a9ac1602091a2f0902c2841942f8dd739562ef6ebbd35894fa445e6a28d748f3c645936914acbdafc8fa59330149ee5ef0738657d8e78d5cf4af5bd26e37ab6b SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild deleted file mode 100644 index bab228e77f5..00000000000 --- a/sci-biology/gatk/gatk-2.4.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -EANT_BUILD_TARGET="dist" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" - -inherit java-pkg-2 java-ant-2 vcs-snapshot - -DESCRIPTION="The Genome Analysis Toolkit" -HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"; -SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=">=virtual/jre-1.6" -DEPEND="${RDEPEND}" - -src_prepare() { - java-pkg-2_src_prepare - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die -} - -src_install() { - java-pkg_dojar dist/*.jar - java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar - java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar -} diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml deleted file mode 100644 index 8c1bb65774c..00000000000 --- a/sci-biology/gatk/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">broadgsa/gatk</remote-id> - </upstream> -</pkgmetadata>
