* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar/
@ 2016-06-23 15:26 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-06-23 15:26 UTC (permalink / raw
To: gentoo-commits
commit: 3372b8cbc1e81f2e39d8bc5247ee9176abfe90bb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 15:26:06 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 15:26:06 2016 +0000
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 0000000..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 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/jannovar/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar/
@ 2016-06-23 16:44 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-06-23 16:44 UTC (permalink / raw
To: gentoo-commits
commit: 246f843671d207583568dc6420a80c4156a0b2b6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 16:44:23 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 16:44:23 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=246f8436
sci-biology/jannovar: improve ebuild, still does not work
Package-Manager: portage-2.2.28
sci-biology/jannovar/jannovar-0.16.ebuild | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild b/sci-biology/jannovar/jannovar-0.16.ebuild
index 9dcbd17..c67b789 100644
--- a/sci-biology/jannovar/jannovar-0.16.ebuild
+++ b/sci-biology/jannovar/jannovar-0.16.ebuild
@@ -29,7 +29,8 @@ src_compile(){
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
+ 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
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar/
@ 2016-11-15 20:19 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-11-15 20:19 UTC (permalink / raw
To: gentoo-commits
commit: 3bd45176e875ab2b69e36a4d430dbb4b5410fb3d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 15 20:18:48 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 15 20:18:48 2016 +0000
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
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar/
@ 2016-12-04 20:15 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-12-04 20:15 UTC (permalink / raw
To: gentoo-commits
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
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2016-12-04 20:15 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-12-04 20:15 [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2016-11-15 20:19 Martin Mokrejs
2016-06-23 16:44 Martin Mokrejs
2016-06-23 15:26 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox