[gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/
commit: 7395e580724ff8e6c42f83b063e71fea97f4069d
Author: Aisha Tammy aisha cc>
AuthorDate: Tue Sep 22 11:08:25 2020 +
Commit: Aisha Tammy aisha cc>
CommitDate: Tue Sep 22 11:08:25 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7395e580
sci-biology/picard: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy aisha.cc>
sci-biology/picard/files/2.2.2-build.xml.patch | 115 -
sci-biology/picard/metadata.xml| 16
sci-biology/picard/picard-1.141.ebuild | 72
sci-biology/picard/picard-2.18.2.ebuild| 62 -
sci-biology/picard/picard-2.2.2.ebuild | 53
sci-biology/picard/picard-.ebuild | 57
6 files changed, 375 deletions(-)
diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch
b/sci-biology/picard/files/2.2.2-build.xml.patch
deleted file mode 100644
index 278c4a1a4..0
--- a/sci-biology/picard/files/2.2.2-build.xml.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-diff --git a/build.xml b/build.xml
-index f0b98ab..14ff7f7 100755
a/build.xml
-+++ b/build.xml
-@@ -83,15 +83,6 @@
-
-
-
--
--
--
--
--
--
--
--
--
-
-
-
-@@ -117,53 +108,21 @@
-
-
-
--
--
--
--
--
--
--
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--
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--
-
-
-
--
--
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-
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-
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-
--
-
-
-
--
-
-
-
--
-
-
-
-@@ -292,15 +251,11 @@
-
-
-
--
--
--
-
-
-
-
-
--
-
-
-
-@@ -396,13 +351,9 @@
-
-
-
--
--
--
-
-
-
--
-
-
-
-@@ -508,10 +459,8 @@
- description="Default build target">
-
-
--
-
-
--
-
-
-
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
deleted file mode 100644
index 1d81f108f..0
--- a/sci-biology/picard/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-
- er...@gentoo.org
- Johann Schmitz (ercpe)
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- broadinstitute/picard
- picard
-
-
diff --git a/sci-biology/picard/picard-1.141.ebuild
b/sci-biology/picard/picard-1.141.ebuild
deleted file mode 100644
index 68b10a73d..0
--- a/sci-biology/picard/picard-1.141.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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
"${S}"/src/tests/java/net/sf/samtools || d
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: c745e42833996f3ceceb7f701baddbe5fe1da566
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Apr 12 15:18:08 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 12 15:18:08 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c745e428
sci-biology/picard: use EGIT_COMMIT to fetch by a release tag
Closes: https://bugs.gentoo.org/653012
Package-Manager: Portage-2.3.27, Repoman-2.3.9
sci-biology/picard/picard-2.18.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/picard/picard-2.18.2.ebuild
b/sci-biology/picard/picard-2.18.2.ebuild
index 24ed178ce..9292b1e19 100644
--- a/sci-biology/picard/picard-2.18.2.ebuild
+++ b/sci-biology/picard/picard-2.18.2.ebuild
@@ -12,7 +12,7 @@ DESCRIPTION="Java-based command-line utilities that
manipulate SAM/BAM/CRAM/VCF
HOMEPAGE="http://picard.sourceforge.net
http://broadinstitute.github.io/picard";
EGIT_REPO_URI="https://github.com/broadinstitute/picard.git";
-EGIT_BRANCH="${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"
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: ff9e6f5b5058cf7f019d76a428ed03421e2d1f91
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Apr 12 11:51:10 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 12 11:51:10 2018 +
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() {
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: ec1391c4ee1f08e4d81b785d50afee9f9f774866
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Apr 12 11:33:10 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 12 11:33:10 2018 +
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-.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-.ebuild
b/sci-biology/picard/picard-.ebuild
index c61316fbd..57bbfdb9f 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.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
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 32cd1f6f1c693d74575f0c0b5be30bf4d61c1999
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Apr 12 11:22:01 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 12 11:22:01 2018 +
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..0
--- 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 "${S}"/javadoc
-#}
diff --git a/sci-biology/picard/picard-2.17.11.ebuild
b/sci-biology/picard/picard-2.17.11.ebuild
new file mode 100644
index 0..636bf879c
--- /dev/null
+++ b/sci-biology/picard/picard-2.17.11.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
+
+inherit git-r3 java-pkg-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate
SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+ http://broadinstitute.github.io/picard";
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git";
+EGIT_BRANCH="${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
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 3fbc1ba7f4498b4999af3ed8fa51545a953c08a8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jul 28 19:15:48 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jul 28 20:05:19 2017 +
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() {
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 71f2c86d5a0e5da102b434d963f2636dad1ec949
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Feb 23 22:22:51 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Feb 23 22:22:51 2017 +
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
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 2361c03b44c7290b229cae0bf23b8ec1b7742c18
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 24 19:04:13 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 24 19:04:13 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2361c03b
sci-biology/picard-: reintroduce src_prepare(), drop ant dependencies
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/picard/picard-.ebuild | 9 ++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index 2bc65f1..050e03e 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.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
$HOME/.m2/
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 530a6b57a5e0398a0d9b90925dae62d9a7c00302
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 24 18:48:16 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 24 18:48:16 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=530a6b57
sci-biology/picard-: do not apply the 2.2.2-build.xml.patch
Current git checkouts contain a fake build.xml which instructs
users to use gradle instead of ant.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/picard/picard-.ebuild | 5 -
1 file changed, 5 deletions(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index e3f22b9..2bc65f1 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.ebuild
@@ -36,11 +36,6 @@ EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
-java_prepare() {
- default
- epatch "${FILESDIR}"/${PV}-build.xml.patch
-}
-
src_compile(){
# work around gradle writing $HOME/.gradle, requiring $HOME/.git and
$HOME/.m2/
# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: da0b020931c3075b2afe18448145eecd90e148e6
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 24 18:43:27 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 24 18:43:27 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=da0b0209
Revert "sci-biology/picard-: apply the 2.2.2 patch to drop bundled htsjdk"
This reverts commit 1bd613187ee8a70163d0d21bbe5ea726f53c5490.
Weird, on two hosts this patch does not apply because the build.xml
is updated. Somehow I have "old" git checkout on my dev machine
although all are at commit 3800c8218b8e4c75a4db14f97b409dbcc3dcaaa8.
Will fix the - ebuild in a moment.
sci-biology/picard/picard-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index ccc0062..e3f22b9 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.ebuild
@@ -38,7 +38,7 @@
EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
java_prepare() {
default
- epatch "${FILESDIR}"/2.2.2-build.xml.patch
+ epatch "${FILESDIR}"/${PV}-build.xml.patch
}
src_compile(){
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 1bd613187ee8a70163d0d21bbe5ea726f53c5490
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 24 18:35:15 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 24 18:35:15 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1bd61318
sci-biology/picard-: 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-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index e3f22b9..ccc0062 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.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 "${FILESDIR}"/2.2.2-build.xml.patch
}
src_compile(){
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 4ded557f598731a54f12134b26083685a6e1
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 20 23:24:38 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 20 23:24:38 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4ded557e
sci-biology/picard: still not working ebuild for current gradle-based build
system
https://github.com/broadinstitute/picard/issues/693
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/picard/picard-.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index a75aa88..e3f22b9 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.ebuild
@@ -38,13 +38,13 @@
EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
java_prepare() {
default
- rm -r src/ src/test/java/* || die
epatch "${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
}
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 82677591400b7f727933d4a67387f5cf9ba52a8d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 20 12:03:46 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 20 12:03:46 2017 +
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-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/picard/picard-.ebuild
b/sci-biology/picard/picard-.ebuild
index 3df5d98..a75aa88 100644
--- a/sci-biology/picard/picard-.ebuild
+++ b/sci-biology/picard/picard-.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
}
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 716ca9a7f85713e713e0f975ed61cbce194a0a67
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 11 23:22:39 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 11 23:22:39 2017 +
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-.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="${WORKDIR}" ./gradlew || die
}
#src_install() {
diff --git a/sci-biology/picard/picard-2.8.1.ebuild
b/sci-biology/picard/picard-.ebuild
similarity index 68%
copy from sci-biology/picard/picard-2.8.1.ebuild
copy to sci-biology/picard/picard-.ebuild
index 4d09e8d..3df5d98 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-.ebuild
@@ -4,14 +4,15 @@
EAPI="6"
-JAVA_PKG_IUSE="doc source"
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
-inherit java-pkg-2 java-ant-2
+inherit git-r3 java-pkg-2 java-ant-2
DESCRIPTION="Java-based command-line utilities that manipulate
SAM/BAM/CRAM/VCF files"
HOMEPAGE="http://picard.sourceforge.net
http://broadinstitute.github.io/picard";
-SRC_URI="https://github.com/broadinstitute/picard/archive/${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
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: f700625100d351a1ca36b068ac06cc66f90cf7dc
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 10 23:02:05 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 10 23:02:05 2017 +
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
+#}
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/
commit: bec93ffba2d6dd56c7b10338771a91490bf1ce28
Author: Johann Schmitz gentoo org>
AuthorDate: Sun Apr 24 06:15:26 2016 +
Commit: Justin Lecher gentoo org>
CommitDate: Sun Apr 24 06:15:26 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bec93ffb
sci-biology/picard: brought ebuild for 2.2.2 to a somewhat workable state.
Dropped test execution for now.
Package-Manager: portage-2.2.26
sci-biology/picard/files/2.2.2-build.xml.patch | 115 +
sci-biology/picard/picard-2.2.2.ebuild | 48 +++
2 files changed, 129 insertions(+), 34 deletions(-)
diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch
b/sci-biology/picard/files/2.2.2-build.xml.patch
new file mode 100644
index 000..278c4a1
--- /dev/null
+++ b/sci-biology/picard/files/2.2.2-build.xml.patch
@@ -0,0 +1,115 @@
+diff --git a/build.xml b/build.xml
+index f0b98ab..14ff7f7 100755
+--- a/build.xml
b/build.xml
+@@ -83,15 +83,6 @@
+
+
+
+-
+-
+-
+-
+-
+-
+-
+-
+-
+
+
+
+@@ -117,53 +108,21 @@
+
+
+
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+
+
+
+-
+-
+-
+-
+-
+
+
+
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+
+
+
+-
+
+
+
+-
+
+
+
+-
+
+
+
+@@ -292,15 +251,11 @@
+
+
+
+-
+-
+-
+
+
+
+
+
+-
+
+
+
+@@ -396,13 +351,9 @@
+
+
+
+-
+-
+-
+
+
+
+-
+
+
+
+@@ -508,10 +459,8 @@
+ description="Default build target">
+
+
+-
+
+
+-
+
+
+
diff --git a/sci-biology/picard/picard-2.2.2.ebuild
b/sci-biology/picard/picard-2.2.2.ebuild
index b9e6917..c43b52c 100644
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ b/sci-biology/picard/picard-2.2.2.ebuild
@@ -2,73 +2,53 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI="5"
+EAPI="6"
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+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://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=""
+KEYWORDS="~amd64 ~x86"
-CDEPEND="dev-java/snappy:1.0
+CDEPEND="dev-java/snappy:1.1
dev-java/cofoja:0
dev-java/commons-jexl:2
- dev-java/ant-core:0"
+ dev-java/ant-core:0
+ dev-java/htsjdk: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"
+EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
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
"${S}"/src/tests/java/net/sf/samtools || die
+ default
+ rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
+ epatch "${FILESDIR}"/${PV}-build.xml.patch
}
src_install() {
cd dist || die
- for i in *-${PV}.jar; do
- java-pkg_newjar $i ${i/-${PV}/}
- rm $i || die
- done
+ java-pkg_dojar ${PN}.jar
+ java-pkg_dojar ${PN}-lib.jar
- java-pkg_dojar *.jar
- for i in *.jar; do
- java-pkg_dolauncher ${i/.jar/} --jar $i;
- done
+ java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
use source && java
[gentoo-commits] proj/sci:master commit in: sci-biology/picard/
commit: 8e2cf825955ffa033248c1092a341a7ad5dea2ec
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Apr 22 14:07:45 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 22 14:07:45 2016 +
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 000..513e863
--- /dev/null
+++ b/sci-biology/picard/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+
+ er...@gentoo.org
+ Johann Schmitz (ercpe)
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
+ picard
+
+
diff --git a/sci-biology/picard/picard-1.141.ebuild
b/sci-biology/picard/picard-1.141.ebuild
new file mode 100644
index 000..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 000..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
+
+
