commit: d0fcff8a955005d6edf20a3e019ab83d0f0a7864 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sun Jan 23 12:55:20 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sun Jan 23 12:55:20 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d0fcff8a
sci-biology/cramtools: remove old java package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/pilon-bin/metadata.xml | 12 ------------ sci-biology/pilon-bin/pilon-bin-1.24.ebuild | 29 ----------------------------- 3 files changed, 42 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 275d7f3fc..1440925e0 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -56,7 +56,6 @@ sci-biology/conrad sci-libs/jhdf5 # ancient java, can't update due to gradle/maven limitation dev-java/htsjdk -sci-biology/pilon-bin sci-misc/opennlp-maxent # Andrew Ammerlaan <andrewammerl...@gentoo.org (13 Jan 2022) diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/pilon-bin/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>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild deleted file mode 100644 index 49d15366f..000000000 --- a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 - -DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs" -HOMEPAGE=" - https://github.com/broadinstitute/pilon - https://github.com/broadinstitute/pilon/wiki"; -SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -# contains bundled sbt-assembly module -DEPEND=">=virtual/jdk-1.7:*" -RDEPEND="${DEPEND} - >=virtual/jre-1.7:* - >=dev-java/htsjdk-1.130" - -S="${WORKDIR}" - -src_install(){ - cp -p "${DISTDIR}"/pilon-${PV}.jar . || die - java-pkg_dojar pilon-${PV}.jar -}
