subject:"\[gentoo\-commits\] proj\/sci\:master commit in\: sci\-biology\/jannovar\/"

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

2021-01-19 Thread Andrew Ammerlaan

commit: 89e43de4283587a68e29f49392474fbc59c23b73
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Tue Jan 19 13:04:18 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Tue Jan 19 13:04:18 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=89e43de4

sci-biology/jannovar-bin: version bump 0.35, unmask

remove non-bin version, maven is not supported by portage

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 ...annovar-bin-0.17.ebuild => jannovar-bin-0.35.ebuild} | 17 +++--
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild 
b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
similarity index 71%
rename from sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
rename to sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
index 4544eaab8..1b3a90297 100644
--- a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
@@ -1,27 +1,25 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 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
+HOMEPAGE="https://jannovar.readthedocs.io/en/master/;
+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"
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
 
 S="${WORKDIR}"
 
@@ -30,7 +28,6 @@ src_install(){
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
 }

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

2016-12-04 Thread Martin Mokrejs

commit: 18cc3c3dfef3fb76ed1be70c6726b57e5f40f337
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Dec  4 20:15:06 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Dec  4 20:15:06 2016 +
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..000
--- 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 000..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
+}

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

2016-12-04 Thread Martin Mokrejs

commit: ab03f1ed818e7a64731b1634cb37f28aba3617c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Dec  4 20:10:19 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Dec  4 20:10:19 2016 +
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
 }

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

2016-11-15 Thread Martin Mokrejs

commit: b2815a91492bff320b83e10cd510b04b2186de27
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Nov 15 20:20:03 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Nov 15 20:20:03 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2815a91

sci-biology/Jannovar-bin: replaced by sci-biology/jannovar, deleting

 .../Jannovar-bin/Jannovar-bin-20150503.ebuild  | 30 --
 sci-biology/Jannovar-bin/metadata.xml  | 12 -
 2 files changed, 42 deletions(-)

diff --git a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild 
b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
deleted file mode 100644
index 09efa5d..000
--- a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 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/contao/index.php/jannovar.html;
-SRC_URI="http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/Jannovar.jar
 -> Jannovar-bin-20150503.jar
-   
http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/JannovarTutorial.pdf
 -> JannovarTutorial.pdf
-   
http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/tutorial.tgz
 -> Jannovar_tutorial.tgz"
-
-# https://github.com/charite/jannovar
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
-
-S="${WORKDIR}"
-
-src_install(){
-   cp "${DISTDIR}"/Jannovar-bin-20150503.jar Jannovar-bin.jar
-   java-pkg_newjar Jannovar-bin.jar
-   java-pkg_dolauncher Jannovar-bin --jar Jannovar-bin.jar
-}

diff --git a/sci-biology/Jannovar-bin/metadata.xml 
b/sci-biology/Jannovar-bin/metadata.xml
deleted file mode 100644
index 1699e58..000
--- a/sci-biology/Jannovar-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-  
-mmokr...@fold.natur.cuni.cz
-Martin Mokrejs
-  
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-  
-

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

2016-11-15 Thread Martin Mokrejs

commit: 3bd45176e875ab2b69e36a4d430dbb4b5410fb3d
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Nov 15 20:18:48 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Nov 15 20:18:48 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bd45176

sci-biology/jannovar: working ebuild, although maven re-fetches 95MB of its deps

Package-Manager: portage-2.3.2

 sci-biology/jannovar/jannovar-0.16.ebuild | 43 +--
 1 file changed, 35 insertions(+), 8 deletions(-)

diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild 
b/sci-biology/jannovar/jannovar-0.16.ebuild
index c67b789..5b13048 100644
--- a/sci-biology/jannovar/jannovar-0.16.ebuild
+++ b/sci-biology/jannovar/jannovar-0.16.ebuild
@@ -16,21 +16,48 @@ 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:*"
-RDEPEND=">=virtual/jre-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 || die
+   mvn package -Dmaven.test.skip.exec=true -DskipTests=true 
-Duser.home="${HOME}" || die
 }
 
 src_install(){
-   mvn install -Dmaven.test.skip.exec=true || die
-   java-pkg_dojar jannovar-cli.jar
-   java-pkg_dolauncher jannovar-cli --jar jannovar-cli.jar
-   java-pkg_dojar jped-cli.jar
-   java-pkg_dolauncher jped-cli --jar jped-cli.jar
+   # 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
 }

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

2016-06-23 Thread Martin Mokrejs

commit: a30c6ba70f9f17451b5a5d0d481c0f0f28d17e7b
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Jun 23 16:37:07 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jun 23 16:37:07 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a30c6ba7

sci-biology/jannovar-bin: add KEYWORDS, works now

Package-Manager: portage-2.2.28

 sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 13 +
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild 
b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
index aee7faa..4d56e65 100644
--- a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -14,7 +14,7 @@ 
SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-c
 
 LICENSE="BSD-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 
 DEPEND=">=virtual/jdk-1.6"
@@ -22,12 +22,9 @@ RDEPEND=">=virtual/jre-1.6"
 
 S="${WORKDIR}"
 
-# BUG: the two jar file soverwrite each other somehow during install
 src_install(){
-   cp "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli-bin.jar
-   java-pkg_newjar jannovar-cli-bin.jar
-   java-pkg_dolauncher jannovar-bin --jar jannovar-cli-"${PV}".jar
-   cp "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli-bin.jar
-   java-pkg_newjar jped-cli-bin.jar
-   java-pkg_dolauncher jped-cli-bin --jar jped-cli-"${PV}".jar
+   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
 }

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

2016-06-23 Thread Martin Mokrejs

commit: 3372b8cbc1e81f2e39d8bc5247ee9176abfe90bb
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Jun 23 15:26:06 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jun 23 15:26:06 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3372b8cb

sci-biology/jannovar: first attempt at a new package

Package-Manager: portage-2.2.28

 sci-biology/jannovar/jannovar-0.16.ebuild | 35 +++
 sci-biology/jannovar/metadata.xml | 12 +++
 2 files changed, 47 insertions(+)

diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild 
b/sci-biology/jannovar/jannovar-0.16.ebuild
new file mode 100644
index 000..9dcbd17
--- /dev/null
+++ b/sci-biology/jannovar/jannovar-0.16.ebuild
@@ -0,0 +1,35 @@
+# 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/contao/index.php/jannovar.html;
+SRC_URI="https://github.com/charite/jannovar/archive/v0.16.tar.gz -> 
${P}.tar.gz"
+
+# https://github.com/charite/jannovar
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6
+   dev-java/maven-bin:*"
+RDEPEND=">=virtual/jre-1.6"
+
+# 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
+src_compile(){
+   mvn package -Dmaven.test.skip.exec=true -DskipTests=true || die
+}
+
+src_install(){
+   mvn install -Dmaven.test.skip.exec=true || die
+   dojar *.jar
+   java-pkg_newjar jannovar-bin.jar
+   java-pkg_dolauncher jannovar-bin --jar jannovar-bin.jar
+}

diff --git a/sci-biology/jannovar/metadata.xml 
b/sci-biology/jannovar/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/jannovar/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
+  
+

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

2016-06-23 Thread Martin Mokrejs

commit: 5b8e34465714552fcfb87a2bce4b6ecb2ac216b8
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Jun 23 15:15:48 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jun 23 15:15:48 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b8e3446

sci-biology/jannovar-bin: renamed package; version bump

Package-Manager: portage-2.2.28

 sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 28 +++
 sci-biology/jannovar-bin/metadata.xml | 12 ++
 2 files changed, 40 insertions(+)

diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild 
b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
new file mode 100644
index 000..fc706b8
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -0,0 +1,28 @@
+# 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/v0.16/jannovar-cli-0.16.jar;
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}"
+
+src_install(){
+   cp "${DISTDIR}"/jannovar-cli-0.16.jar jannovar-bin.jar
+   java-pkg_newjar jannovar-bin.jar
+   java-pkg_dolauncher jannovar-bin --jar jannovar-bin.jar
+}

diff --git a/sci-biology/jannovar-bin/metadata.xml 
b/sci-biology/jannovar-bin/metadata.xml
new file mode 100644
index 000..1699e58
--- /dev/null
+++ b/sci-biology/jannovar-bin/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
+  
+

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

2015-05-05 Thread Martin Mokrejs

commit: df363e30c8033d85992c787537f5864836ebf4b4
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Tue May  5 14:29:02 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Tue May  5 14:29:02 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=df363e30

sci-biology/Jannovar-bin: new package

Package-Manager: portage-2.2.18

 sci-biology/Jannovar-bin/ChangeLog |  9 +++
 .../Jannovar-bin/Jannovar-bin-20150503.ebuild  | 30 ++
 sci-biology/Jannovar-bin/metadata.xml  |  9 +++
 3 files changed, 48 insertions(+)

diff --git a/sci-biology/Jannovar-bin/ChangeLog 
b/sci-biology/Jannovar-bin/ChangeLog
new file mode 100644
index 000..5a6ec92
--- /dev/null
+++ b/sci-biology/Jannovar-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/Jannovar-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Jannovar-bin-20150503 (05 May 2015)
+
+  05 May 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  +Jannovar-bin-20150503.ebuild, +metadata.xml:
+  sci-biology/Jannovar-bin: new package

diff --git a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild 
b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
new file mode 100644
index 000..890494a
--- /dev/null
+++ b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION=Exome annotation tool
+HOMEPAGE=http://compbio.charite.de/contao/index.php/jannovar.html;
+SRC_URI=http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/Jannovar.jar
 - Jannovar-bin-20150503.jar
+   
http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/JannovarTutorial.pdf
 - JannovarTutorial.pdf
+   
http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/tutorial.tgz
 - Jannovar_tutorial.tgz
+
+# https://github.com/charite/jannovar
+LICENSE=BSD-2
+SLOT=0
+KEYWORDS=~amd64
+IUSE=
+
+DEPEND==virtual/jdk-1.7
+RDEPEND==virtual/jre-1.7
+
+S=${WORKDIR}
+
+src_install(){
+   cp ${DISTDIR}/Jannovar-bin-20150503.jar Jannovar-bin.jar
+   java-pkg_newjar Jannovar-bin.jar
+   java-pkg_dolauncher Jannovar-bin --jar Jannovar-bin.jar
+}

diff --git a/sci-biology/Jannovar-bin/metadata.xml 
b/sci-biology/Jannovar-bin/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/Jannovar-bin/metadata.xml
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+  herdsci-biology/herd
+  maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+  /maintainer
+/pkgmetadata

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

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

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

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

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

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

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

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

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

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