commit: 86e4e275f65c24db50b905dbfe2d1b873ebbfe50 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sun Jan 23 12:54:56 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sun Jan 23 12:54:56 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=86e4e275
sci-biology/cramtools: remove old java package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/cramtools/cramtools-3.0.ebuild | 34 ------------------------------ sci-biology/cramtools/metadata.xml | 15 ------------- 3 files changed, 50 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index cfebeb744..275d7f3fc 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/cramtools sci-biology/pilon-bin sci-misc/opennlp-maxent diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild deleted file mode 100644 index b57f4fb26..000000000 --- a/sci-biology/cramtools/cramtools-3.0.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java tools and APIs for efficient compression of sequence read data" -HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit - https://github.com/enasequence/cramtools"; -SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=virtual/jdk-1.7:* - dev-java/ant-core - dev-java/htsjdk" -RDEPEND=" - ${DEPEND} - >=virtual/jre-1.7:*" - -# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk? -# https://github.com/enasequence/cramtools/issues/58 -# https://github.com/enasequence/cramtools/issues/59 -src_compile(){ - ant -f build/build.xml runnable || die -} - -src_install() { - java-pkg_newjar "${P}.jar" "${PN}.jar" -} diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml deleted file mode 100644 index 5a55ad312..000000000 --- a/sci-biology/cramtools/metadata.xml +++ /dev/null @@ -1,15 +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> - <upstream> - <remote-id type="github">enasequence/cramtools</remote-id> - </upstream> -</pkgmetadata>
