[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/jannovar/

[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/jannovar/

[Andrew Ammerlaan]

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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">charite/jannovar</remote-id>
-	</upstream>
-</pkgmetadata>