[gentoo-commits] repo/gentoo:master commit in: profiles/, sci-biology/gatk/

[gentoo-commits] repo/gentoo:master commit in: profiles/, sci-biology/gatk/

[Sam James]

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 <soap@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 <mgorny@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-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">broadgsa/gatk</remote-id>
-  </upstream>
-</pkgmetadata>