[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
