[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/, sci-biology/gatk/files/
commit: 09664039e99b1f7d3a0b36ee6f0ae3993be2904b
Author: Horea Christian chymera eu>
AuthorDate: Mon Sep 28 07:33:53 2020 +
Commit: Horea Christian gmail com>
CommitDate: Mon Sep 28 07:33:53 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=09664039
sci-biology/gatk: removed package with missing dep
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian chymera.eu>
sci-biology/gatk/files/settings.xml | 9
sci-biology/gatk/gatk-3.8.1.ebuild | 102
sci-biology/gatk/gatk-.ebuild | 82 -
sci-biology/gatk/metadata.xml | 11
4 files changed, 204 deletions(-)
diff --git a/sci-biology/gatk/files/settings.xml
b/sci-biology/gatk/files/settings.xml
deleted file mode 100644
index 9527ec0b7..0
--- a/sci-biology/gatk/files/settings.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-http://maven.apache.org/SETTINGS/1.0.0;
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance;
- xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
- https://maven.apache.org/xsd/settings-1.0.0.xsd;>
- ${user.home}/.m2/repository
- false
- false
- true
-
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild
b/sci-biology/gatk/gatk-3.8.1.ebuild
deleted file mode 100644
index 9ad24d86c..0
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
-
-MY_PV=${PV/.1/-1} # convert 3.8.1 to 3.8-1
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git; # git tree for <=gatk-3
-# check out 3.8-1 branch but using a proper commit, not ${MY_PV}
-# https://github.com/broadinstitute/gatk/issues/4685#issuecomment-383188772
-EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
-
-DEPEND="
- >=virtual/jdk-1.6
- dev-java/maven-bin:* || ( dev-java/netbeans-java )
- dev-java/cofoja
- "
-RDEPEND="
- >=virtual/jre-1.6
- >=sci-biology/SnpEff-2.0.5
- "
-
-#S="${WORKDIR}/${PN}-${MY_PV}"
-
-# https://maven.apache.org/settings.html
-# The two settings files are located at:
-# The Maven installation directory: $M2_HOME/conf/settings.xml
-# The user's home directory: ${user.home}/.m2/settings.xml
-#
-# localRepository: This value is the path of this build system's local
repository.
-#The default value is ${user.home}/.m2/repository. This element is
especially
-#useful for a main build server allowing all logged-in users to build from
a
-#common local repository.
-# interactiveMode: true if Maven should attempt to interact with the user for
input,
-#false if not. Defaults to true.
-# usePluginRegistry: true if Maven should use the
${user.home}/.m2/plugin-registry.xml
-#file to manage plugin versions, defaults to false. Note that for the
current version
-#of Maven 2.0, the plugin-registry.xml file should not be depended upon.
Consider it
-#dormant for now.
-# offline: true if this build system should operate in offline mode, defaults
to false.
-#This element is useful for build servers which cannot connect to a remote
repository,
-#either because of network setup or security reasons.
-
-src_prepare() {
- mvn clean -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
- sed -e
's#mvn_args="#mvn_args="-Dmaven.repo.local=${WORKDIR}/.m2/repository #' -i
ant-bridge.sh || die
- mkdir -p "${WORKDIR}"/.m2/repository || die
- cp "${FILESDIR}"/settings.xml "${WORKDIR}"/.m2/repository/ || die
- #export M2_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
- #export MAVEN_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
- export M2="${WORKDIR}"/.m2/repository # not recognized?
- #export MAVEN_OPTS="-Xms256m -Xmx512m" # works but not needed actually
- sh ant-bridge.sh || die # BUG: this downloads and compiles lot of stuff
- java-pkg-2_src_prepare
-}
-
-src_install() {
- mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
- # Java QA Notice: installing versioned jar 'gatk-tools-public-3.8-1.jar'
- # Java QA Notice: installing versioned jar
'gatk-queue-extensions-generator-3.8-1.jar'
- # Java QA Notice: installing versioned jar 'gatk-engine-3.8-1.jar'
- # Java QA Notice: installing versioned jar
'gatk-queue-extensions-public-3.8-1.jar'
- # Java QA Notice: installing versioned jar 'gatk-utils-3.8-1.jar'
- # Java QA Notice: installing versioned jar 'gatk-queue-3.8-1.jar'
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/
commit: b118528394ea931b4732e27b266bc38a5d1c0ff1
Author: Horea Christian chymera eu>
AuthorDate: Sun Sep 13 23:12:53 2020 +
Commit: Horea Christian gmail com>
CommitDate: Sun Sep 13 23:12:53 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1185283
sci-biology/gatk: updated license, copyright, and ebuild style
Signed-off-by: Horea Christian chymera.eu>
sci-biology/gatk/gatk-3.8.1.ebuild | 8 +++-
sci-biology/gatk/gatk-.ebuild | 13 +
2 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild
b/sci-biology/gatk/gatk-3.8.1.ebuild
index f46c1d322..9ad24d86c 100644
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ b/sci-biology/gatk/gatk-3.8.1.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=5
@@ -17,19 +17,17 @@ EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
LICENSE="MIT"
SLOT="0"
-IUSE=""
KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
-COMMON_DEPS=""
DEPEND="
>=virtual/jdk-1.6
dev-java/maven-bin:* || ( dev-java/netbeans-java )
dev-java/cofoja
- ${COMMON_DEPS}"
+ "
RDEPEND="
>=virtual/jre-1.6
>=sci-biology/SnpEff-2.0.5
- ${COMMON_DEPS}"
+ "
#S="${WORKDIR}/${PN}-${MY_PV}"
diff --git a/sci-biology/gatk/gatk-.ebuild
b/sci-biology/gatk/gatk-.ebuild
index fc9db8986..70d42cb0a 100644
--- a/sci-biology/gatk/gatk-.ebuild
+++ b/sci-biology/gatk/gatk-.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=5
@@ -14,16 +14,13 @@ EGIT_CLONE_TYPE="mirror"
# building outside of git is not possible,
# see https://github.com/broadinstitute/picard/issues/605
#
-#
+#
# must run 'git clone https://github.com/broadinstitute/gatk.git gatk'
# see https://github.com/broadinstitute/gatk/issues/4687
-LICENSE="BSD-3" # since gatk-4
+LICENSE="BSD" # since gatk-4
SLOT="0"
-IUSE=""
-KEYWORDS="" # 148.19 MB git download and 134MB "${W}"/.m2 download
-COMMON_DEPS=""
# gatk-4 needs java-1.8
DEPEND="
>=virtual/jdk-1.8
@@ -31,12 +28,12 @@ DEPEND="
>=dev-vcs/git-lfs-1.1.0
>=dev-java/maven-bin-3.1:* || ( dev-java/netbeans-java )
dev-java/cofoja
- ${COMMON_DEPS}"
+ "
RDEPEND="
>=virtual/jre-1.8
>=sci-biology/SnpEff-2.0.5
>=dev-lang/R-3.2.5
- ${COMMON_DEPS}"
+ "
#S="${WORKDIR}/${PN}-${MY_PV}"
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/
commit: d7d0ec9c245ade97fc147c8688378783e1a63d5c
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Apr 21 19:15:54 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 21 19:15:54 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7d0ec9c
sci-biology/gatk: comment out copy command
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/gatk/gatk-.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/gatk/gatk-.ebuild
b/sci-biology/gatk/gatk-.ebuild
index 2bf5af325..fc9db8986 100644
--- a/sci-biology/gatk/gatk-.ebuild
+++ b/sci-biology/gatk/gatk-.ebuild
@@ -77,7 +77,9 @@ src_install() {
cd build/libs || die
java-pkg_dojar "${PN}".jar
java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
- java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+ #java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
#use source && java-pkg_dosrc "${S}"/src/java/*
#use doc && java-pkg_dojavadoc "${S}"/javadoc
+ #
+ # install a bash-completion script gatk-completion.sh into proper place
}
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/
commit: 4900a804981bab3e6abfc55143b9b519d89e9780
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Apr 20 22:22:37 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 20 22:22:37 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4900a804
sci-biology/gatk: oops, drop KEYWORDS
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/gatk/gatk-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/gatk/gatk-.ebuild
b/sci-biology/gatk/gatk-.ebuild
index 09c4abc0f..2bf5af325 100644
--- a/sci-biology/gatk/gatk-.ebuild
+++ b/sci-biology/gatk/gatk-.ebuild
@@ -21,7 +21,7 @@ EGIT_CLONE_TYPE="mirror"
LICENSE="BSD-3" # since gatk-4
SLOT="0"
IUSE=""
-KEYWORDS="~amd64" # 148.19 MB git download and 134MB "${W}"/.m2 download
+KEYWORDS="" # 148.19 MB git download and 134MB "${W}"/.m2 download
COMMON_DEPS=""
# gatk-4 needs java-1.8
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/
commit: 6e0e46ff5c3099e4b206fc30d76a564bb4135b21
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Apr 20 21:39:48 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 20 21:39:48 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e0e46ff
sci-biology/gatk: cleanup gatk-3.8.1 and improve a bit gatk-
The gatk- ebuild does not work because it calls 'git fetch' instead
of 'git clone'. See https://github.com/broadinstitute/gatk/issues/4687
and https://github.com/broadinstitute/gatk#building for more details.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/gatk/gatk-3.8.1.ebuild | 7 ++--
sci-biology/gatk/gatk-.ebuild | 80 +++---
2 files changed, 61 insertions(+), 26 deletions(-)
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild
b/sci-biology/gatk/gatk-3.8.1.ebuild
index b2610a770..f46c1d322 100644
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ b/sci-biology/gatk/gatk-3.8.1.ebuild
@@ -5,11 +5,12 @@ EAPI=5
inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
-# fetch -3.8-1.tar.gz
-MY_PV=${PV/.1/-1}
+MY_PV=${PV/.1/-1} # convert 3.8.1 to 3.8-1
DESCRIPTION="The Genome Analysis Toolkit"
HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git;
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git; # git tree for <=gatk-3
+# check out 3.8-1 branch but using a proper commit, not ${MY_PV}
+# https://github.com/broadinstitute/gatk/issues/4685#issuecomment-383188772
EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
# building outside of git is not possible,
# see https://github.com/broadinstitute/picard/issues/605
diff --git a/sci-biology/gatk/gatk-.ebuild
b/sci-biology/gatk/gatk-.ebuild
index 4b6d7f1cc..09c4abc0f 100644
--- a/sci-biology/gatk/gatk-.ebuild
+++ b/sci-biology/gatk/gatk-.ebuild
@@ -1,49 +1,83 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
-EANT_BUILD_TARGET="dist"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-inherit git-2 java-pkg-2
+inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
DESCRIPTION="The Genome Analysis Toolkit"
HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git;
+EGIT_REPO_URI="https://github.com/broadinstitute/gatk.git; # git tree for
>=gatk-4
+EGIT_CLONE_TYPE="mirror"
+# building outside of git is not possible,
+# see https://github.com/broadinstitute/picard/issues/605
+#
+#
+# must run 'git clone https://github.com/broadinstitute/gatk.git gatk'
+# see https://github.com/broadinstitute/gatk/issues/4687
-LICENSE="MIT"
+LICENSE="BSD-3" # since gatk-4
SLOT="0"
IUSE=""
-KEYWORDS=""
+KEYWORDS="~amd64" # 148.19 MB git download and 134MB "${W}"/.m2 download
COMMON_DEPS=""
+# gatk-4 needs java-1.8
DEPEND="
- >=virtual/jdk-1.6
- dev-vcs/git
- dev-java/maven-bin:*
+ >=virtual/jdk-1.8
+ >=dev-vcs/git-2.5
+ >=dev-vcs/git-lfs-1.1.0
+ >=dev-java/maven-bin-3.1:* || ( dev-java/netbeans-java )
dev-java/cofoja
${COMMON_DEPS}"
RDEPEND="
- >=virtual/jre-1.6
+ >=virtual/jre-1.8
>=sci-biology/SnpEff-2.0.5
+ >=dev-lang/R-3.2.5
${COMMON_DEPS}"
+#S="${WORKDIR}/${PN}-${MY_PV}"
+
+# https://maven.apache.org/settings.html
+# The two settings files are located at:
+# The Maven installation directory: $M2_HOME/conf/settings.xml
+# The user's home directory: ${user.home}/.m2/settings.xml
+#
+# localRepository: This value is the path of this build system's local
repository.
+#The default value is ${user.home}/.m2/repository. This element is
especially
+#useful for a main build server allowing all logged-in users to build from
a
+#common local repository.
+# interactiveMode: true if Maven should attempt to interact with the user for
input,
+#false if not. Defaults to true.
+# usePluginRegistry: true if Maven should use the
${user.home}/.m2/plugin-registry.xml
+#file to manage plugin versions, defaults to false. Note that for the
current version
+#of Maven 2.0, the plugin-registry.xml file should not be depended upon.
Consider it
+#dormant for now.
+# offline: true if this build system should operate in offline mode, defaults
to false.
+#This element is useful for build servers which cannot connect to a remote
repository,
+#either because of network setup or security reasons.
+
src_prepare() {
- sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
- java-pkg-2_src_prepare
+ default
}
-src_install() {
- mvn install
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/files/, sci-biology/gatk/
commit: cb99f31b0e528eda8ac02259b562a85f247d7d06
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Apr 20 19:36:13 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 20 19:36:13 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb99f31b
sci-biology/gatk: version bump to 3.8-1
Bump to the latest version before commandline syntax has been
changed (in gatk-4). The package builds at the cost of downloading
608.21 MiB during git tree download and 134MB when download maven
jar files into "${W}"/.m2 directory.
The ebuild works around permissions issue when mvn attempts to
access $HOME/.m2 which is outside sandbox.
The ebuild installs individual jar files and porobably using a
different target we could get out the GenomeAnalysisTK.jar
file as upstream actually releases as its binary.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/gatk/files/settings.xml | 9
sci-biology/gatk/gatk-3.6.ebuild| 47
sci-biology/gatk/gatk-3.8.1.ebuild | 103
3 files changed, 112 insertions(+), 47 deletions(-)
diff --git a/sci-biology/gatk/files/settings.xml
b/sci-biology/gatk/files/settings.xml
new file mode 100644
index 0..9527ec0b7
--- /dev/null
+++ b/sci-biology/gatk/files/settings.xml
@@ -0,0 +1,9 @@
+http://maven.apache.org/SETTINGS/1.0.0;
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance;
+ xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
+ https://maven.apache.org/xsd/settings-1.0.0.xsd;>
+ ${user.home}/.m2/repository
+ false
+ false
+ true
+
diff --git a/sci-biology/gatk/gatk-3.6.ebuild b/sci-biology/gatk/gatk-3.6.ebuild
deleted file mode 100644
index bdbf14e9b..0
--- a/sci-biology/gatk/gatk-3.6.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-EANT_BUILD_TARGET="dist"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-inherit java-pkg-2 java-ant-2 vcs-snapshot
-
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
-SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-COMMON_DEPS=""
-DEPEND="
- >=virtual/jdk-1.6
- dev-java/maven-bin:*
- dev-java/cofoja
- ${COMMON_DEPS}"
-RDEPEND="
- >=virtual/jre-1.6
- >=sci-biology/SnpEff-2.0.5
- ${COMMON_DEPS}"
-
-src_prepare() {
- sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
- java-pkg-2_src_prepare
-}
-
-src_install() {
- mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
- find public -name \*.jar | grep -v tests | grep -v cofoja | while read
f; do \
- java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned
jar 'gatk-tools-public-3.6.jar'
- done
-}
-
-pkg_postinst(){
- einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
- einfo "installation layout gets more testing"
-}
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild
b/sci-biology/gatk/gatk-3.8.1.ebuild
new file mode 100644
index 0..b2610a770
--- /dev/null
+++ b/sci-biology/gatk/gatk-3.8.1.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
+
+# fetch -3.8-1.tar.gz
+MY_PV=${PV/.1/-1}
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git;
+EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
+# building outside of git is not possible,
+# see https://github.com/broadinstitute/picard/issues/605
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
+
+COMMON_DEPS=""
+DEPEND="
+ >=virtual/jdk-1.6
+ dev-java/maven-bin:* || ( dev-java/netbeans-java )
+ dev-java/cofoja
+ ${COMMON_DEPS}"
+RDEPEND="
+ >=virtual/jre-1.6
+ >=sci-biology/SnpEff-2.0.5
+ ${COMMON_DEPS}"
+
+#S="${WORKDIR}/${PN}-${MY_PV}"
+
+# https://maven.apache.org/settings.html
+# The two settings files are located at:
+# The Maven installation directory: $M2_HOME/conf/settings.xml
+# The user's home directory: ${user.home}/.m2/settings.xml
+#
+# localRepository: This value is the path of this build system's local
repository.
+#The default value is ${user.home}/.m2/repository. This element is
especially
+#useful for a main build server allowing all logged-in users to build from
a
+#common local repository.
+# interactiveMode: true if Maven should attempt to interact with the user for
input,
+#
[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/
commit: 07d6f1753d0063d948bfc29120bec3d7894aa013
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jul 27 16:21:21 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jul 27 16:21:21 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=07d6f175
sci-biology/gatk: upstream uses maven instead of ant, adjust ebuilds
Package-Manager: portage-2.2.28
sci-biology/gatk/gatk-3.6.ebuild | 48 +
sci-biology/gatk/gatk-.ebuild | 50 +++
sci-biology/gatk/metadata.xml | 11 +
3 files changed, 109 insertions(+)
diff --git a/sci-biology/gatk/gatk-3.6.ebuild b/sci-biology/gatk/gatk-3.6.ebuild
new file mode 100644
index 000..d05d2f7
--- /dev/null
+++ b/sci-biology/gatk/gatk-3.6.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit java-pkg-2 java-ant-2 vcs-snapshot
+
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
+SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND="
+ >=virtual/jdk-1.6
+ dev-java/maven-bin:*
+ dev-java/cofoja
+ ${COMMON_DEPS}"
+RDEPEND="
+ >=virtual/jre-1.6
+ >=sci-biology/SnpEff-2.0.5
+ ${COMMON_DEPS}"
+
+src_prepare() {
+ sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+ find public -name \*.jar | grep -v tests | grep -v cofoja | while read
f; do \
+ java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned
jar 'gatk-tools-public-3.6.jar'
+ done
+}
+
+pkg_postinst(){
+ einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
+ einfo "installation layout gets more testing"
+}
diff --git a/sci-biology/gatk/gatk-.ebuild
b/sci-biology/gatk/gatk-.ebuild
new file mode 100644
index 000..cdc6646
--- /dev/null
+++ b/sci-biology/gatk/gatk-.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit git-2 java-pkg-2
+
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit;
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git;
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+COMMON_DEPS=""
+DEPEND="
+ >=virtual/jdk-1.6
+ dev-vcs/git
+ dev-java/maven-bin:*
+ dev-java/cofoja
+ ${COMMON_DEPS}"
+RDEPEND="
+ >=virtual/jre-1.6
+ >=sci-biology/SnpEff-2.0.5
+ ${COMMON_DEPS}"
+
+src_prepare() {
+ sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+ find public -name \*.jar | grep -v tests | grep -v cofoja | while read
f; do \
+ java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned
jar 'gatk-tools-public-3.6.jar'
+ done
+}
+
+pkg_postinst(){
+ einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
+ einfo "installation layout gets more testing"
+}
diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
new file mode 100644
index 000..8c1bb65
--- /dev/null
+++ b/sci-biology/gatk/metadata.xml
@@ -0,0 +1,11 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
+broadgsa/gatk
+
+
