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

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

[Horea Christian]

commit:     b118528394ea931b4732e27b266bc38a5d1c0ff1
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 13 23:12:53 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 13 23:12:53 2020 +0000
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 <chr <AT> chymera.eu>

 sci-biology/gatk/gatk-3.8.1.ebuild |  8 +++-----
 sci-biology/gatk/gatk-9999.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-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index fc9db8986..70d42cb0a 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.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/

[Martin Mokrejs]

commit:     d7d0ec9c245ade97fc147c8688378783e1a63d5c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 19:15:54 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 19:15:54 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7d0ec9c

sci-biology/gatk: comment out copy&pasted command

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/gatk/gatk-9999.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index 2bf5af325..fc9db8986 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.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/

[Martin Mokrejs]

commit:     4900a804981bab3e6abfc55143b9b519d89e9780
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 20 22:22:37 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 20 22:22:37 2018 +0000
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-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index 09c4abc0f..2bf5af325 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.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/

[Martin Mokrejs]

commit:     6e0e46ff5c3099e4b206fc30d76a564bb4135b21
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 20 21:39:48 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 20 21:39:48 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e0e46ff

sci-biology/gatk: cleanup gatk-3.8.1 and improve a bit gatk-9999

The gatk-9999 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-9999.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-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index 4b6d7f1cc..09c4abc0f 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.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 -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
+src_compile(){
+	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	# make jure SDK-1.8 is available, JRE-1.8 is not enough
+	#
+	# https://github.com/broadinstitute/gatk#building
+	# gradlew tragets are bundle, localJar, sparkJar, ...
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug bundle || die
 }
 
-pkg_postinst(){
-	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
-	einfo "installation layout gets more testing"
+src_install() {
+	cd build/libs || die
+	java-pkg_dojar "${PN}".jar
+	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
+	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+	#use source && java-pkg_dosrc "${S}"/src/java/*
+	#use doc && java-pkg_dojavadoc "${S}"/javadoc
 }

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

[Martin Mokrejs]

commit:     07d6f1753d0063d948bfc29120bec3d7894aa013
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul 27 16:21:21 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul 27 16:21:21 2016 +0000
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-9999.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 0000000..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-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
new file mode 100644
index 0000000..cdc6646
--- /dev/null
+++ b/sci-biology/gatk/gatk-9999.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 0000000..8c1bb65
--- /dev/null
+++ b/sci-biology/gatk/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">broadgsa/gatk</remote-id>
+  </upstream>
+</pkgmetadata>