commit: ab03f1ed818e7a64731b1634cb37f28aba3617c1 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Dec 4 20:10:19 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Dec 4 20:10:19 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab03f1ed
sci-biology/jannovar: version bump, seems only one jar can be directly executed https://github.com/charite/jannovar/issues/218 https://github.com/charite/jannovar/releases Package-Manager: portage-2.3.2 .../{jannovar-0.16.ebuild => jannovar-0.17.ebuild} | 26 +++++++++------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild b/sci-biology/jannovar/jannovar-0.17.ebuild similarity index 54% rename from sci-biology/jannovar/jannovar-0.16.ebuild rename to sci-biology/jannovar/jannovar-0.17.ebuild index 5b13048..1e8ca0d 100644 --- a/sci-biology/jannovar/jannovar-0.16.ebuild +++ b/sci-biology/jannovar/jannovar-0.17.ebuild @@ -8,7 +8,7 @@ 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/v0.16.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/charite/jannovar/archive/v"${PV}".tar.gz -> ${P}.tar.gz" # https://github.com/charite/jannovar LICENSE="BSD-2" @@ -46,18 +46,14 @@ src_install(){ # maven download 95MB from the network into "${PORTAGE_BUILDDIR}/homedir/" export M2="${HOME}" mvn install -Dmaven.test.skip.exec=true -Duser.home="${HOME}" || die - java-pkg_dojar jannovar-cli/target/jannovar-cli-0.16.jar - java-pkg_dolauncher jannovar-cli --jar jannovar-cli-0.16.jar - java-pkg_dojar jped-cli/target/jped-cli-0.16.jar - java-pkg_dolauncher jped-cli --jar jped-cli-0.16.jar - #java-pkg_dojar jannovar-hgvs/target/jannovar-hgvs-0.16.jar - #java-pkg_dolauncher jannovar-hgvs --jar jannovar-hgvs-0.16.jar - #java-pkg_dojar jannovar-htsjdk/target/jannovar-htsjdk-0.16.jar - #java-pkg_dolauncher jannovar-htsjdk --jar jannovar-htsjdk-0.16.jar - #java-pkg_dojar jannovar-core/target/jannovar-core-0.16.jar - #java-pkg_dolauncher jannovar-core --jar jannovar-core-0.16.jar - #java-pkg_dojar jannovar-filter/target/jannovar-filter-0.16.jar - #java-pkg_dolauncher jannovar-filter --jar jannovar-filter-0.16.jar - #java-pkg_dojar jannovar-inheritance-checker/target/jannovar-inheritance-checker-0.16.jar - #java-pkg_dolauncher jannovar-inheritance-checker --jar jannovar-inheritance-checker-0.16.jar + # 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 }
