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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-11 23:27 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-11 23:27 UTC (permalink / raw
  To: gentoo-commits

commit:     f700625100d351a1ca36b068ac06cc66f90cf7dc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 23:02:05 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 23:02:05 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7006251

sci-biology/picard: upstream moved from ant to gradle build system

Building does not work for me due to:
 https://github.com/broadinstitute/picard/issues/693

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-1.141.ebuild             |  2 +-
 sci-biology/picard/picard-2.2.2.ebuild             |  2 +-
 .../{picard-2.2.2.ebuild => picard-2.8.1.ebuild}   | 29 +++++++++++++---------
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild
index ab65edb..b84d91d 100644
--- a/sci-biology/picard/picard-1.141.ebuild
+++ b/sci-biology/picard/picard-1.141.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 

diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild
index c43b52c..f0cc489 100644
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ b/sci-biology/picard/picard-2.2.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 

diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.8.1.ebuild
similarity index 63%
copy from sci-biology/picard/picard-2.2.2.ebuild
copy to sci-biology/picard/picard-2.8.1.ebuild
index c43b52c..4d09e8d 100644
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ b/sci-biology/picard/picard-2.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -16,7 +16,7 @@ SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.t
 LICENSE="MIT"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
 
 CDEPEND="dev-java/snappy:1.1
 	dev-java/cofoja:0
@@ -41,14 +41,19 @@ java_prepare() {
 	epatch "${FILESDIR}"/${PV}-build.xml.patch
 }
 
-src_install() {
-	cd dist || die
-
-	java-pkg_dojar ${PN}.jar
-	java-pkg_dojar ${PN}-lib.jar
-
-	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
+src_compile(){
+	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
 }
+
+#src_install() {
+#	cd dist || die
+#	java-pkg_dojar ${PN}.jar
+#	java-pkg_dojar ${PN}-lib.jar
+#	
+#	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+#	
+#	use source && java-pkg_dosrc "${S}"/src/java/*
+#	use doc && java-pkg_dojavadoc "${S}"/javadoc
+#}


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2018-04-12 15:18 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2018-04-12 15:18 UTC (permalink / raw
  To: gentoo-commits

commit:     c745e42833996f3ceceb7f701baddbe5fe1da566
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 15:18:08 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 15:18:08 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c745e428

sci-biology/picard: use EGIT_COMMIT to fetch by a release tag

Closes: https://bugs.gentoo.org/653012
Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/picard/picard-2.18.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-2.18.2.ebuild b/sci-biology/picard/picard-2.18.2.ebuild
index 24ed178ce..9292b1e19 100644
--- a/sci-biology/picard/picard-2.18.2.ebuild
+++ b/sci-biology/picard/picard-2.18.2.ebuild
@@ -12,7 +12,7 @@ DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF
 HOMEPAGE="http://picard.sourceforge.net
 	http://broadinstitute.github.io/picard"
 EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
-EGIT_BRANCH="${PV}"
+EGIT_COMMIT="${PV}"
 # building outside of git is not possible,
 # see https://github.com/broadinstitute/picard/issues/605
 #SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2018-04-12 11:51 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2018-04-12 11:51 UTC (permalink / raw
  To: gentoo-commits

commit:     ff9e6f5b5058cf7f019d76a428ed03421e2d1f91
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 11:51:10 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 11:51:10 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff9e6f5b

sci-biology/picard: do not compile testsuite by default

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/picard/picard-2.18.2.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-2.18.2.ebuild b/sci-biology/picard/picard-2.18.2.ebuild
index 636bf879c..24ed178ce 100644
--- a/sci-biology/picard/picard-2.18.2.ebuild
+++ b/sci-biology/picard/picard-2.18.2.ebuild
@@ -46,7 +46,8 @@ src_compile(){
 	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
 	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die
+	# see more gradlew arg options in build.xml, especially jar versus shadowJar
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug compileJava jar || die
 }
 
 src_install() {


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2018-04-12 11:33 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2018-04-12 11:33 UTC (permalink / raw
  To: gentoo-commits

commit:     ec1391c4ee1f08e4d81b785d50afee9f9f774866
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 11:33:10 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 11:33:10 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ec1391c4

sci-biology/picard: bring in the latest release actually

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/picard/{picard-2.17.11.ebuild => picard-2.18.2.ebuild} | 0
 sci-biology/picard/picard-9999.ebuild                              | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-2.17.11.ebuild b/sci-biology/picard/picard-2.18.2.ebuild
similarity index 100%
rename from sci-biology/picard/picard-2.17.11.ebuild
rename to sci-biology/picard/picard-2.18.2.ebuild

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index c61316fbd..57bbfdb9f 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6


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* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2018-04-12 11:22 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2018-04-12 11:22 UTC (permalink / raw
  To: gentoo-commits

commit:     32cd1f6f1c693d74575f0c0b5be30bf4d61c1999
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 11:22:01 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 11:22:01 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=32cd1f6f

sci-biology/picard: version bump (not working yet)

Bug: https://github.com/broadinstitute/picard/issues/605
Bug: https://bugs.gentoo.org/653012
Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/picard/picard-2.10.2.ebuild  | 58 ------------------------------
 sci-biology/picard/picard-2.17.11.ebuild | 61 ++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+), 58 deletions(-)

diff --git a/sci-biology/picard/picard-2.10.2.ebuild b/sci-biology/picard/picard-2.10.2.ebuild
deleted file mode 100644
index bddadedbb..000000000
--- a/sci-biology/picard/picard-2.10.2.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
-	http://broadinstitute.github.io/picard"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/snappy:1.1
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/ant-core:0
-	dev-java/htsjdk:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
-
-java_prepare() {
-	default
-	rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
-	epatch "${FILESDIR}"/${PV}-build.xml.patch
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die
-}
-
-#src_install() {
-#	cd dist || die
-#	java-pkg_dojar ${PN}.jar
-#	java-pkg_dojar ${PN}-lib.jar
-#
-#	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-#
-#	use source && java-pkg_dosrc "${S}"/src/java/*
-#	use doc && java-pkg_dojavadoc "${S}"/javadoc
-#}

diff --git a/sci-biology/picard/picard-2.17.11.ebuild b/sci-biology/picard/picard-2.17.11.ebuild
new file mode 100644
index 000000000..636bf879c
--- /dev/null
+++ b/sci-biology/picard/picard-2.17.11.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
+
+inherit git-r3 java-pkg-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
+EGIT_BRANCH="${PV}"
+# building outside of git is not possible,
+# see https://github.com/broadinstitute/picard/issues/605
+#SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+CDEPEND="dev-java/snappy:1.1
+	dev-java/cofoja:0
+	dev-java/commons-jexl:2
+	dev-java/htsjdk:0"
+
+DEPEND=">=virtual/jdk-1.8
+	${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,htsjdk"
+
+src_prepare() {
+	default
+}
+
+src_compile(){
+	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	# make jure SDK-1.8 is available, JRE-1.8 is not enough
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die
+}
+
+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
+}


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-07-28 20:05 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
  To: gentoo-commits

commit:     3fbc1ba7f4498b4999af3ed8fa51545a953c08a8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:15:48 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3fbc1ba7

sci-biology/picard: version bump

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/picard/{picard-2.9.0.ebuild => picard-2.10.2.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-2.9.0.ebuild b/sci-biology/picard/picard-2.10.2.ebuild
similarity index 95%
rename from sci-biology/picard/picard-2.9.0.ebuild
rename to sci-biology/picard/picard-2.10.2.ebuild
index c7a01ba72..bddadedbb 100644
--- a/sci-biology/picard/picard-2.9.0.ebuild
+++ b/sci-biology/picard/picard-2.10.2.ebuild
@@ -43,7 +43,7 @@ java_prepare() {
 src_compile(){
 	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die
 }
 
 #src_install() {


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-02-23 22:23 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-02-23 22:23 UTC (permalink / raw
  To: gentoo-commits

commit:     71f2c86d5a0e5da102b434d963f2636dad1ec949
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 23 22:22:51 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 23 22:22:51 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=71f2c86d

sci-biology/picard: version bump

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/{picard-2.8.1.ebuild => picard-2.9.0.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.9.0.ebuild
similarity index 100%
rename from sci-biology/picard/picard-2.8.1.ebuild
rename to sci-biology/picard/picard-2.9.0.ebuild


^ permalink raw reply	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-24 19:04 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-24 19:04 UTC (permalink / raw
  To: gentoo-commits

commit:     2361c03b44c7290b229cae0bf23b8ec1b7742c18
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 24 19:04:13 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 24 19:04:13 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2361c03b

sci-biology/picard-9999: reintroduce src_prepare(), drop ant dependencies

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-9999.ebuild | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index 2bc65f1..050e03e 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -7,7 +7,7 @@ EAPI="6"
 #JAVA_PKG_IUSE="doc source"
 JAVA_PKG_IUSE=""
 
-inherit git-r3 java-pkg-2 java-ant-2
+inherit git-r3 java-pkg-2
 
 DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
 HOMEPAGE="http://picard.sourceforge.net
@@ -22,7 +22,6 @@ KEYWORDS=""
 CDEPEND="dev-java/snappy:1.1
 	dev-java/cofoja:0
 	dev-java/commons-jexl:2
-	dev-java/ant-core:0
 	dev-java/htsjdk:0"
 
 DEPEND=">=virtual/jdk-1.8
@@ -34,7 +33,11 @@ RDEPEND=">=virtual/jre-1.8
 EANT_BUILD_TARGET="all"
 EANT_NEEDS_TOOLS="true"
 JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
+EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,htsjdk"
+
+src_prepare() {
+	default
+}
 
 src_compile(){
 	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-24 18:48 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-24 18:48 UTC (permalink / raw
  To: gentoo-commits

commit:     530a6b57a5e0398a0d9b90925dae62d9a7c00302
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 24 18:48:16 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 24 18:48:16 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=530a6b57

sci-biology/picard-9999: do not apply the 2.2.2-build.xml.patch

Current git checkouts contain a fake build.xml which instructs
users to use gradle instead of ant.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-9999.ebuild | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index e3f22b9..2bc65f1 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -36,11 +36,6 @@ EANT_NEEDS_TOOLS="true"
 JAVA_ANT_REWRITE_CLASSPATH="true"
 EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
 
-java_prepare() {
-	default
-	epatch "${FILESDIR}"/${PV}-build.xml.patch
-}
-
 src_compile(){
 	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-24 18:45 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-24 18:45 UTC (permalink / raw
  To: gentoo-commits

commit:     da0b020931c3075b2afe18448145eecd90e148e6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 24 18:43:27 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 24 18:43:27 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da0b0209

Revert "sci-biology/picard-9999: apply the 2.2.2 patch to drop bundled htsjdk"

This reverts commit 1bd613187ee8a70163d0d21bbe5ea726f53c5490.

Weird, on two hosts this patch does not apply because the build.xml
is updated. Somehow I have "old" git checkout on my dev machine
although all are at commit 3800c8218b8e4c75a4db14f97b409dbcc3dcaaa8.

Will fix the -9999 ebuild in a moment.

 sci-biology/picard/picard-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index ccc0062..e3f22b9 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -38,7 +38,7 @@ EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
 
 java_prepare() {
 	default
-	epatch "${FILESDIR}"/2.2.2-build.xml.patch
+	epatch "${FILESDIR}"/${PV}-build.xml.patch
 }
 
 src_compile(){


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-24 18:35 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-24 18:35 UTC (permalink / raw
  To: gentoo-commits

commit:     1bd613187ee8a70163d0d21bbe5ea726f53c5490
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 24 18:35:15 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 24 18:35:15 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1bd61318

sci-biology/picard-9999: apply the 2.2.2 patch to drop bundled htsjdk

This is probably not needed as currently it uses gradlew to build but
the patch still applies to build.xml and maybe somebody will manage to
resurrect the ant-based build process.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index e3f22b9..ccc0062 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -38,7 +38,7 @@ EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
 
 java_prepare() {
 	default
-	epatch "${FILESDIR}"/${PV}-build.xml.patch
+	epatch "${FILESDIR}"/2.2.2-build.xml.patch
 }
 
 src_compile(){


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-20 23:24 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-20 23:24 UTC (permalink / raw
  To: gentoo-commits

commit:     4ded557eeeef598731a54f12134b26083685a6e1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 20 23:24:38 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 20 23:24:38 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4ded557e

sci-biology/picard: still not working ebuild for current gradle-based build system

https://github.com/broadinstitute/picard/issues/693

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index a75aa88..e3f22b9 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -38,13 +38,13 @@ EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
 
 java_prepare() {
 	default
-	rm -r src/ src/test/java/* || die
 	epatch "${FILESDIR}"/${PV}-build.xml.patch
 }
 
 src_compile(){
-	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
+	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	# make jure SDK-1.8 is available, JRE-1.8 is not enough
 	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-20 12:04 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-20 12:04 UTC (permalink / raw
  To: gentoo-commits

commit:     82677591400b7f727933d4a67387f5cf9ba52a8d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 20 12:03:46 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 20 12:03:46 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=82677591

sci-biology/picard: adjust to test directory now moved elsewhere in src stree

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
index 3df5d98..a75aa88 100644
--- a/sci-biology/picard/picard-9999.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -38,7 +38,7 @@ EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
 
 java_prepare() {
 	default
-	rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
+	rm -r src/ src/test/java/* || die
 	epatch "${FILESDIR}"/${PV}-build.xml.patch
 }
 


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2017-01-11 23:27 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-11 23:27 UTC (permalink / raw
  To: gentoo-commits

commit:     716ca9a7f85713e713e0f975ed61cbce194a0a67
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 11 23:22:39 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 11 23:22:39 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=716ca9a7

sci-biology/picard-2.8.1: version bump, do not compile tests by default

Also add a live ebuild so we can test upstream with the gradle build
system.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-2.8.1.ebuild             |  2 +-
 .../{picard-2.8.1.ebuild => picard-9999.ebuild}    | 29 +++++++++++-----------
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.8.1.ebuild
index 4d09e8d..7f8b3fd 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-2.8.1.ebuild
@@ -44,7 +44,7 @@ java_prepare() {
 src_compile(){
 	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 
 #src_install() {

diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-9999.ebuild
similarity index 68%
copy from sci-biology/picard/picard-2.8.1.ebuild
copy to sci-biology/picard/picard-9999.ebuild
index 4d09e8d..3df5d98 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -4,14 +4,15 @@
 
 EAPI="6"
 
-JAVA_PKG_IUSE="doc source"
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
 
-inherit java-pkg-2 java-ant-2
+inherit git-r3 java-pkg-2 java-ant-2
 
 DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
 HOMEPAGE="http://picard.sourceforge.net
 	http://broadinstitute.github.io/picard"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
 
 LICENSE="MIT"
 SLOT="0"
@@ -44,16 +45,16 @@ java_prepare() {
 src_compile(){
 	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 
-#src_install() {
-#	cd dist || die
-#	java-pkg_dojar ${PN}.jar
-#	java-pkg_dojar ${PN}-lib.jar
-#	
-#	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-#	
-#	use source && java-pkg_dosrc "${S}"/src/java/*
-#	use doc && java-pkg_dojavadoc "${S}"/javadoc
-#}
+src_install() {
+	cd build/libs || die
+	java-pkg_dojar "${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
+}


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/
@ 2016-04-22 14:08 Martin Mokrejs
  0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2016-04-22 14:08 UTC (permalink / raw
  To: gentoo-commits

commit:     8e2cf825955ffa033248c1092a341a7ad5dea2ec
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 22 14:07:45 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 22 14:07:45 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e2cf825

sci-biology/picard: preparing last java7-compatible version and one for java8

Package-Manager: portage-2.2.28

 sci-biology/picard/metadata.xml        | 15 +++++++
 sci-biology/picard/picard-1.141.ebuild | 73 +++++++++++++++++++++++++++++++++
 sci-biology/picard/picard-2.2.2.ebuild | 74 ++++++++++++++++++++++++++++++++++
 3 files changed, 162 insertions(+)

diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
new file mode 100644
index 0000000..513e863
--- /dev/null
+++ b/sci-biology/picard/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>ercpe@gentoo.org</email>
+		<name>Johann Schmitz (ercpe)</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">picard</remote-id>
+	</upstream>
+</pkgmetadata>

diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild
new file mode 100644
index 0000000..ab65edb
--- /dev/null
+++ b/sci-biology/picard/picard-1.141.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+JAVA_PKG_IUSE="doc source test"
+WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
+SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0" # 2.2.2 is MIT instead, not sure when it changed away from Apache
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+CDEPEND="dev-java/snappy:1.0
+	dev-java/cofoja:0
+	dev-java/commons-jexl:2
+	dev-java/ant-core:0"
+
+DEPEND=">=virtual/jdk-1.7
+	dev-java/ant-apache-bcel:0
+	test? (
+		dev-java/testng:0
+		dev-lang/R
+	)
+	${CDEPEND}"
+RDEPEND=">=virtual/jre-1.7
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_TEST_TARGET="test"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
+EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
+
+java_prepare() {
+	mkdir -p "${S}"/lib || die
+
+	# TODO: update the patch
+	#epatch "${FILESDIR}"/${PV}-gentoo.patch
+
+	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *-${PV}.jar; do
+		java-pkg_newjar $i ${i/-${PV}/}
+		rm $i || die
+	done
+
+	java-pkg_dojar *.jar
+	for i in *.jar; do
+		java-pkg_dolauncher ${i/.jar/} --jar $i;
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}
+
+src_test() {
+	java-pkg-2_src_test
+}

diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild
new file mode 100644
index 0000000..b9e6917
--- /dev/null
+++ b/sci-biology/picard/picard-2.2.2.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+JAVA_PKG_IUSE="doc source test"
+WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
+SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+CDEPEND="dev-java/snappy:1.0
+	dev-java/cofoja:0
+	dev-java/commons-jexl:2
+	dev-java/ant-core:0"
+
+DEPEND=">=virtual/jdk-1.8
+	dev-java/ant-apache-bcel:0
+	test? (
+		dev-java/testng:0
+		dev-lang/R
+	)
+	${CDEPEND}"
+# >=jdk8u66
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_TEST_TARGET="test"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
+EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
+
+java_prepare() {
+	mkdir -p "${S}"/lib || die
+
+	# TODO: update the old patch
+	#epatch "${FILESDIR}"/${PV}-gentoo.patch
+
+	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *-${PV}.jar; do
+		java-pkg_newjar $i ${i/-${PV}/}
+		rm $i || die
+	done
+
+	java-pkg_dojar *.jar
+	for i in *.jar; do
+		java-pkg_dolauncher ${i/.jar/} --jar $i;
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}
+
+src_test() {
+	java-pkg-2_src_test
+}


^ permalink raw reply related	[flat|nested] 15+ messages in thread

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