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