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

[Martin Mokrejs]

commit:     18cc3c3dfef3fb76ed1be70c6726b57e5f40f337
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec  4 20:15:06 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec  4 20:15:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=18cc3c3d

sci-biology/jannovar-bin: version bump

Provided sci-biology/jannovar download through maven lots of dependencies
and anyway uses plenty of upstream jar file this sci-biology/jannovar-bin
package is probably better choice due to size of downloads and security

Package-Manager: portage-2.3.2

 sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 30 ------------------
 sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild | 37 +++++++++++++++++++++++
 2 files changed, 37 insertions(+), 30 deletions(-)

diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
deleted file mode 100644
index 4d56e65..0000000
--- a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Exome annotation tool"
-HOMEPAGE="http://compbio.charite.de
-	https://github.com/charite/jannovar"
-SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-cli-${PV}.jar
-	https://repo1.maven.org/maven2/de/charite/compbio/jped-cli/${PV}/jped-cli-${PV}.jar"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6"
-RDEPEND=">=virtual/jre-1.6"
-
-S="${WORKDIR}"
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
-	java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
-	java-pkg_newjar "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli.jar
-	java-pkg_dolauncher jped-cli-bin --jar jped-cli.jar
-}

diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
new file mode 100644
index 0000000..e6f392e
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool (upstream jar binaries)"
+HOMEPAGE="http://compbio.charite.de
+	https://github.com/charite/jannovar"
+SRC_URI="https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-vardbs/${PV}/jannovar-vardbs-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-htsjdk/${PV}/jannovar-htsjdk-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-inheritance-checker/${PV}/jannovar-inheritance-checker-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-core/${PV}/jannovar-core-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-hgvs/${PV}/jannovar-hgvs-${PV}.jar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6"
+RDEPEND=">=virtual/jre-1.6"
+
+S="${WORKDIR}"
+
+src_install(){
+	java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
+	java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-vardbs-"${PV}".jar jannovar-vardbs.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-htsjdk-"${PV}".jar jannovar-htsjdk.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-inheritance-checker-"${PV}".jar jannovar-inheritance-checker.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-core-${PV}.jar jannovar-core.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-hgvs-${PV}.jar jannovar-hgvs.jar
+}