[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
commit: 5ea2483a3e1f329d32d540e515f8d326573b9c45 Author: Horea Christian chymera eu> AuthorDate: Sun May 14 04:19:39 2023 + Commit: Horea Christian gmail com> CommitDate: Sun May 14 04:19:44 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ea2483a sci-biology/rtg-tools: treeclean dev-java/jython dependency has been removed by e4d717fb45ff9bf0ae328dccee5dd761630c3436 on ::gentoo :( Signed-off-by: Horea Christian chymera.eu> sci-biology/rtg-tools/metadata.xml | 15 --- sci-biology/rtg-tools/rtg-tools-3.12.ebuild | 63 - 2 files changed, 78 deletions(-) diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml deleted file mode 100644 index 026053b60..0 --- a/sci-biology/rtg-tools/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ - -http://www.gentoo.org/dtd/metadata.dtd";> - - - mmokr...@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biol...@gentoo.org - Gentoo Biology Project - - - RealTimeGenomics/rtg-tools - - diff --git a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild deleted file mode 100644 index a07f55539..0 --- a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild +++ /dev/null @@ -1,63 +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="Manipulate and analyze VCF files" -HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"; -SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=virtual/jdk-1.8:* - >=dev-java/ant-core-1.9 - dev-java/jython" -RDEPEND="${DEPEND} - >=virtual/jre-1.8:*" - -src_compile(){ - ant zip-nojre || die -} - -# "${S}"/lib/sam-2.9.1.jar -# "${S}"/lib/findbugs-annotations.jar -# "${S}"/lib/findbugs-jsr305.jar -# "${S}"/lib/velocity-tools-generic.jar -# "${S}"/lib/RPlot.jar -# "${S}"/lib/commons-collections-3.2.1.jar -# "${S}"/lib/velocity-1.7.jar -# "${S}"/lib/commons-compress-1.4.1.jar -# "${S}"/lib/commons-lang-2.4.jar -# "${S}"/lib/jumble-annotations.jar -# "${S}"/lib/sam-2.9.1-src.jar -# "${S}"/lib/gzipfix.jar -# "${S}"/buildLib/ant-contrib-1.0b3.jar -# "${S}"/buildLib/handlechecker.jar -# "${S}"/testLib/hamcrest-core-1.3.jar -# "${S}"/testLib/junit.jar -# "${S}"/testLib/spelling.jar - -src_install(){ - dobin installer/rtg - insinto /usr/share/"${PN}" - doins build/rtg-tools.jar - doins lib/gzipfix.jar - dodoc installer/resources/tools/RTGOperationsManual.pdf - doins -r installer/resources/tools/RTGOperationsManual - dodoc installer/resources/tools/scripts/README.txt - dodoc installer/ReleaseNotes.txt - # TODO - # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip - # file or better the installer/resources/ source directory - # - # install installer/resources/common/scripts/rtg-bash-completion -} - -src_test(){ - ant runalltests || die -}
[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
commit: e79174d58d525ca5f08f787b805af12549ce8bd5 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 13:50:35 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 13:50:35 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e79174d5 sci-biology/rtg-tools: EAPI bump, add keywords Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> .../{rtg-tools-.ebuild => rtg-tools-3.12.ebuild} | 19 +-- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/sci-biology/rtg-tools/rtg-tools-.ebuild b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild similarity index 83% rename from sci-biology/rtg-tools/rtg-tools-.ebuild rename to sci-biology/rtg-tools/rtg-tools-3.12.ebuild index 4f146be70..a07f55539 100644 --- a/sci-biology/rtg-tools/rtg-tools-.ebuild +++ b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild @@ -1,25 +1,24 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit java-pkg-2 java-ant-2 eutils git-r3 +inherit java-pkg-2 java-ant-2 DESCRIPTION="Manipulate and analyze VCF files" HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"; -EGIT_REPO_URI="https://github.com/RealTimeGenomics/rtg-tools.git"; +SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="BSD-2" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="~amd64" DEPEND=" - >=virtual/jdk-1.8:* - >=dev-java/ant-core-1.9 - dev-java/jython" + >=virtual/jdk-1.8:* + >=dev-java/ant-core-1.9 + dev-java/jython" RDEPEND="${DEPEND} - >=virtual/jre-1.8:*" + >=virtual/jre-1.8:*" src_compile(){ ant zip-nojre || die
[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
commit: f51d6ce27e5c393c5c28926cee6d87b89d0e699c Author: Martin Mokrejs gmail com> AuthorDate: Thu Dec 10 11:12:19 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Dec 10 11:13:08 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f51d6ce2 sci-biology/rtg-tools: install missing files The ebuild still needs some cleanup IMO, especially the rtg shell script which writes /etc/rtg.cfg and $bindir needs a fix. But one can run the jar file directly. Package-Manager: Portage-3.0.11, Repoman-3.0.2 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/rtg-tools/rtg-tools-.ebuild | 26 +++--- 1 file changed, 23 insertions(+), 3 deletions(-) diff --git a/sci-biology/rtg-tools/rtg-tools-.ebuild b/sci-biology/rtg-tools/rtg-tools-.ebuild index b658f7c17..4f146be70 100644 --- a/sci-biology/rtg-tools/rtg-tools-.ebuild +++ b/sci-biology/rtg-tools/rtg-tools-.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -16,13 +16,13 @@ IUSE="" DEPEND=" >=virtual/jdk-1.8:* - dev-java/ant-core + >=dev-java/ant-core-1.9 dev-java/jython" RDEPEND="${DEPEND} >=virtual/jre-1.8:*" src_compile(){ - ant runalltests || die + ant zip-nojre || die } # "${S}"/lib/sam-2.9.1.jar @@ -42,3 +42,23 @@ src_compile(){ # "${S}"/testLib/hamcrest-core-1.3.jar # "${S}"/testLib/junit.jar # "${S}"/testLib/spelling.jar + +src_install(){ + dobin installer/rtg + insinto /usr/share/"${PN}" + doins build/rtg-tools.jar + doins lib/gzipfix.jar + dodoc installer/resources/tools/RTGOperationsManual.pdf + doins -r installer/resources/tools/RTGOperationsManual + dodoc installer/resources/tools/scripts/README.txt + dodoc installer/ReleaseNotes.txt + # TODO + # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip + # file or better the installer/resources/ source directory + # + # install installer/resources/common/scripts/rtg-bash-completion +} + +src_test(){ + ant runalltests || die +}
[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
commit: d6910887c28e8d10b591d525a2c30e6588b14344 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Jan 26 12:50:42 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Jan 26 12:50:42 2018 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d6910887 sci-biology/rtg-tools: adjust description Package-Manager: Portage-2.3.20, Repoman-2.3.6 sci-biology/rtg-tools/rtg-tools-.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/rtg-tools/rtg-tools-.ebuild b/sci-biology/rtg-tools/rtg-tools-.ebuild index 30843a98e..b658f7c17 100644 --- a/sci-biology/rtg-tools/rtg-tools-.ebuild +++ b/sci-biology/rtg-tools/rtg-tools-.ebuild @@ -5,7 +5,7 @@ EAPI=6 inherit java-pkg-2 java-ant-2 eutils git-r3 -DESCRIPTION="Manipulate and analyze SAM/BAM/VCF files" +DESCRIPTION="Manipulate and analyze VCF files" HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"; EGIT_REPO_URI="https://github.com/RealTimeGenomics/rtg-tools.git";
[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
commit: cb2c0165a5a3e091ffbbd123a4ab0334a75eed24 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Jan 26 11:05:09 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Jan 26 11:05:09 2018 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb2c0165 sci-biology/rtg-tools: package skeleton Will need to ask upstream to provide common 'compile', 'install' and 'all' targets into https://github.com/RealTimeGenomics/rtg-tools/blob/master/build.xml Any volunteers to unbundle the bundled stuff? At least it is not gradle but good old ant. ;) Package-Manager: Portage-2.3.20, Repoman-2.3.6 sci-biology/rtg-tools/metadata.xml | 12 sci-biology/rtg-tools/rtg-tools-.ebuild | 44 + 2 files changed, 56 insertions(+) diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml new file mode 100644 index 0..138cb7705 --- /dev/null +++ b/sci-biology/rtg-tools/metadata.xml @@ -0,0 +1,12 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + mmokr...@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biol...@gentoo.org + Gentoo Biology Project + + diff --git a/sci-biology/rtg-tools/rtg-tools-.ebuild b/sci-biology/rtg-tools/rtg-tools-.ebuild new file mode 100644 index 0..30843a98e --- /dev/null +++ b/sci-biology/rtg-tools/rtg-tools-.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit java-pkg-2 java-ant-2 eutils git-r3 + +DESCRIPTION="Manipulate and analyze SAM/BAM/VCF files" +HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"; +EGIT_REPO_URI="https://github.com/RealTimeGenomics/rtg-tools.git"; + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + >=virtual/jdk-1.8:* + dev-java/ant-core + dev-java/jython" +RDEPEND="${DEPEND} + >=virtual/jre-1.8:*" + +src_compile(){ + ant runalltests || die +} + +# "${S}"/lib/sam-2.9.1.jar +# "${S}"/lib/findbugs-annotations.jar +# "${S}"/lib/findbugs-jsr305.jar +# "${S}"/lib/velocity-tools-generic.jar +# "${S}"/lib/RPlot.jar +# "${S}"/lib/commons-collections-3.2.1.jar +# "${S}"/lib/velocity-1.7.jar +# "${S}"/lib/commons-compress-1.4.1.jar +# "${S}"/lib/commons-lang-2.4.jar +# "${S}"/lib/jumble-annotations.jar +# "${S}"/lib/sam-2.9.1-src.jar +# "${S}"/lib/gzipfix.jar +# "${S}"/buildLib/ant-contrib-1.0b3.jar +# "${S}"/buildLib/handlechecker.jar +# "${S}"/testLib/hamcrest-core-1.3.jar +# "${S}"/testLib/junit.jar +# "${S}"/testLib/spelling.jar