commit: 1aa3db4971c490674fc92a0eb076c8b5120f1cc4 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 13:05:09 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 13:05:09 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1aa3db49
sci-biology/jannover: drop pack, unsupported build system maven does not work with portage, use the -bin version instead Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/jannovar/jannovar-0.17.ebuild | 58 ------------------------------- sci-biology/jannovar/metadata.xml | 15 -------- 3 files changed, 74 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 31c424659..76b2513eb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -71,4 +71,3 @@ sci-biology/graf-bin sci-biology/hydra-sv sci-biology/ICC sci-biology/IMAGE -sci-biology/jannovar diff --git a/sci-biology/jannovar/jannovar-0.17.ebuild b/sci-biology/jannovar/jannovar-0.17.ebuild deleted file mode 100644 index 7337adbc2..000000000 --- a/sci-biology/jannovar/jannovar-0.17.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 - -DESCRIPTION="Exome annotation tool" -HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"; -SRC_URI="https://github.com/charite/jannovar/archive/v"${PV}".tar.gz -> ${P}.tar.gz" - -# https://github.com/charite/jannovar -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -COMMON_DEPS=" - dev-java/commons-compress - dev-java/commons-io - dev-java/commons-jexl:* - dev-java/commons-logging:0 - dev-java/commons-net - dev-java/guava:* - dev-java/hamcrest-core:* - dev-java/htsjdk - dev-java/ini4j - dev-java/junit:* - dev-java/log4j:0" -DEPEND=">=virtual/jdk-1.6 - dev-java/maven-bin:* - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.6 - ${COMMON_DEPS}" - -# TODO: set a proxy because it downloads data during compile step -# http://jannovar.readthedocs.io/en/master/install.html -# see https://github.com/charite/jannovar/issues/218 -# https://maven.apache.org/settings.html#Proxies -src_compile(){ - mvn package -Dmaven.test.skip.exec=true -DskipTests=true -Duser.home="${HOME}" || die -} - -src_install(){ - # maven download 95MB from the network into "${PORTAGE_BUILDDIR}/homedir/" - export M2="${HOME}" - mvn install -Dmaven.test.skip.exec=true -Duser.home="${HOME}" || die - # jannovar-cli-${PV}.jar includes all libraries (jannovar and others like htsjdk) - java-pkg_dojar jannovar-cli/target/jannovar-cli-"${PV}".jar - java-pkg_dolauncher jannovar-cli --jar jannovar-cli-"${PV}".jar - # original-jannovar-cli-0.17.jar contains only the source files of the specific package - java-pkg_dojar jannovar-cli/target/original-jannovar-cli-"${PV}".jar - java-pkg_dojar jannovar-hgvs/target/jannovar-hgvs-"${PV}".jar - java-pkg_dojar jannovar-htsjdk/target/jannovar-htsjdk-"${PV}".jar - java-pkg_dojar jannovar-core/target/jannovar-core-"${PV}".jar - java-pkg_dojar jannovar-vardbs/target/jannovar-vardbs-"${PV}".jar - java-pkg_dojar jannovar-inheritance-checker/target/jannovar-inheritance-checker-"${PV}".jar -} diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml deleted file mode 100644 index 5e4e28811..000000000 --- a/sci-biology/jannovar/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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">charite/jannovar</remote-id> - </upstream> -</pkgmetadata>
