* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 22+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: d16e20f697612139018c0cf45bf15c05e8681f37
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:23:52 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:23:52 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d16e20f6
sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds
Package-Manager: portage-2.2.17
---
sci-biology/igv/ChangeLog | 6 +++++-
sci-biology/igv/igv-2.0.32.ebuild | 35 -----------------------------------
sci-biology/igv/igv-2.0.35.ebuild | 20 +++++++++++---------
sci-biology/igv/metadata.xml | 10 +++++-----
4 files changed, 21 insertions(+), 50 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 57895e3..8fe0e05 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/igv
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild,
+ igv-2.0.35.ebuild, metadata.xml:
+ sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds
+
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
API bumped, whitespace removal
diff --git a/sci-biology/igv/igv-2.0.32.ebuild b/sci-biology/igv/igv-2.0.32.ebuild
deleted file mode 100644
index 67a0c5b..0000000
--- a/sci-biology/igv/igv-2.0.32.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-WANT_ANT_TASKS="ant-apache-bcel"
-
-inherit subversion java-pkg-2 java-ant-2
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-SRC_URI=""
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-COMMON_DEPS=""
-DEPEND=">=virtual/jdk-1.6
- ${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
- ${COMMON_DEPS}"
-
-src_install() {
- java-pkg_newjar igv.jar
- for i in lib/*.jar; do java-pkg_dojar $i; done
- java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}
diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index a9021e7..e5d4e93 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -17,30 +17,32 @@ inherit subversion java-pkg-2 java-ant-2
DESCRIPTION="Integrative Genomics Viewer"
HOMEPAGE="http://www.broadinstitute.org/igv/"
SRC_URI=""
+
LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64"
+KEYWORDS=""
-COMMON_DEPS="dev-java/batik
+COMMON_DEPS="
+ dev-java/batik
dev-java/absolutelayout
dev-java/jama
dev-java/commons-logging
- dev-java/commons-math
+ dev-java/commons-math:3
dev-java/concurrent-util
dev-java/jcommon
dev-java/jfreechart
dev-java/hdf-java
dev-java/jlfgr
- dev-java/junit
+ dev-java/junit:0
dev-java/log4j
dev-db/mysql-connector-c++
sci-biology/samtools
dev-java/swing-layout
sci-biology/vcftools"
-DEPEND=">=virtual/jdk-1.6
+DEPEND=">=virtual/jdk-1.6:*
${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
+RDEPEND=">=virtual/jre-1.6:*
${COMMON_DEPS}"
src_install() {
@@ -90,8 +92,8 @@ src_install() {
# /usr/share/igv/lib/xml-apis-1.3.04.jar
# /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
cd lib || die
- rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
- cd ..
+ rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die
+ cd .. || die
for i in lib/*.jar; do java-pkg_dojar $i; done
diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/igv/metadata.xml
+++ b/sci-biology/igv/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2017-04-06 22:57 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2017-04-06 22:57 UTC (permalink / raw
To: gentoo-commits
commit: 66aada24067d9d41a6017132c2c567d94bde4eb7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 6 22:57:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 6 22:57:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=66aada24
sci-biology/igv: fix SLOTs in ebuild
Notably because Gentoo has no more guava-17 we depend on never, untested version guava-20.
Upstream does not guarantee IGV will work with newer dependencies properly.
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/igv/igv-2.3.47.ebuild | 6 +++---
sci-biology/igv/igv-2.3.81.ebuild | 18 +++++++++---------
sci-biology/igv/igv-2.3.88.ebuild | 2 +-
sci-biology/igv/igv-2.3.92.ebuild | 2 +-
4 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
index 5349f1eb7..751ad3943 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.47.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
EAPI=5
@@ -40,7 +40,7 @@ COMMON_DEPS="
dev-java/jlfgr:0
dev-java/log4j:0
dev-java/gson:2.2.2
- dev-java/guava:*
+ dev-java/guava:20
dev-java/swing-layout:1
dev-java/jgrapht:0
dev-java/junit:4"
@@ -59,7 +59,7 @@ EANT_NEEDS_TOOLS="true"
EANT_EXTRA_ARGS="-Dnotests=true"
EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
java_prepare() {
mv lib oldlib || die
diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index a000ef8d5..5fabefeb3 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.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
EAPI=5
@@ -36,17 +36,17 @@ COMMON_DEPS="
dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
- dev-java/commons-math:*
- dev-java/commons-jexl:*
+ dev-java/commons-math:2
+ dev-java/commons-jexl:2
dev-java/jcommon:*
- dev-java/jfreechart:*
+ dev-java/jfreechart:1.0
dev-java/jlfgr:0
dev-java/log4j:0
- dev-java/gson:*
- >=dev-java/guava-17:*
- dev-java/swing-layout:*
+ dev-java/gson:2.2.2
+ dev-java/guava:20
+ dev-java/swing-layout:1
dev-java/jgrapht:0
- dev-java/junit:0"
+ dev-java/junit:4"
DEPEND=">=virtual/jdk-1.7
app-arch/unzip
@@ -62,7 +62,7 @@ EANT_NEEDS_TOOLS="true"
EANT_EXTRA_ARGS="-Dnotests=true"
EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
java_prepare() {
mv lib oldlib || die
diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 71298049f..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -43,7 +43,7 @@ COMMON_DEPS="
dev-java/jlfgr:0
dev-java/log4j:0
dev-java/gson:2.2.2
- dev-java/guava:17
+ dev-java/guava:20
dev-java/swing-layout:1
dev-java/jgrapht:0
dev-java/junit:4"
diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
index 71298049f..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -43,7 +43,7 @@ COMMON_DEPS="
dev-java/jlfgr:0
dev-java/log4j:0
dev-java/gson:2.2.2
- dev-java/guava:17
+ dev-java/guava:20
dev-java/swing-layout:1
dev-java/jgrapht:0
dev-java/junit:4"
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2017-04-03 16:18 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2017-04-03 16:18 UTC (permalink / raw
To: gentoo-commits
commit: d384a8e567a575653b5714b4c3643c88ab3fae72
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 3 16:18:02 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 3 16:18:02 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d384a8e5
sci-biology/igv: fix SLOT operators
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/igv/igv-2.3.88.ebuild | 16 ++++++++--------
sci-biology/igv/igv-2.3.92.ebuild | 14 +++++++-------
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 367ff7048..71298049f 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.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
EAPI=5
@@ -36,17 +36,17 @@ COMMON_DEPS="
dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
- dev-java/commons-math:*
- dev-java/commons-jexl:*
+ dev-java/commons-math:2
+ dev-java/commons-jexl:2
dev-java/jcommon:*
- dev-java/jfreechart:*
+ dev-java/jfreechart:1.0
dev-java/jlfgr:0
dev-java/log4j:0
- dev-java/gson:*
- dev-java/guava:*
- dev-java/swing-layout:*
+ dev-java/gson:2.2.2
+ dev-java/guava:17
+ dev-java/swing-layout:1
dev-java/jgrapht:0
- dev-java/junit:*"
+ dev-java/junit:4"
DEPEND=">=virtual/jdk-1.7
app-arch/unzip
diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
index 72b0dcff1..71298049f 100644
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -36,17 +36,17 @@ COMMON_DEPS="
dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
- >=dev-java/commons-math-2:*
- >=dev-java/commons-jexl-2:*
+ dev-java/commons-math:2
+ dev-java/commons-jexl:2
dev-java/jcommon:*
- >=dev-java/jfreechart-1.0:*
+ dev-java/jfreechart:1.0
dev-java/jlfgr:0
dev-java/log4j:0
- >=dev-java/gson-2.2.2:*
- =dev-java/guava-17:*
- >=dev-java/swing-layout-1
+ dev-java/gson:2.2.2
+ dev-java/guava:17
+ dev-java/swing-layout:1
dev-java/jgrapht:0
- >=dev-java/junit-4"
+ dev-java/junit:4"
DEPEND=">=virtual/jdk-1.7
app-arch/unzip
^ permalink raw reply related [flat|nested] 22+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2017-04-03 15:45 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2017-04-03 15:45 UTC (permalink / raw
To: gentoo-commits
commit: c2d81203011805abd24ae7adb6c8afc14ea02949
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 3 15:45:26 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 3 15:45:26 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2d81203
sci-biology/igv: version bump, cannot compile FlowSignalDistributionPanel.java:222
It seem this is related to Gentoo ebuild unbundling some of the bundled libs.
I can compile vanilla sources using ant without this issue.
[javac] Compiling 889 source files to /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/tmp
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:33: warning: NotImplementedException is internal proprietary API and may be removed in a future release
[javac] import sun.reflect.generics.reflectiveObjects.NotImplementedException;
[javac] ^
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
[javac] dataset.addValue(data[j], seriename, cat);
[javac] ^
[javac] class file for org.jfree.util.PublicCloneable not found
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:266: error: cannot access Drawable
[javac] CategoryPlot plot = freechart.getCategoryPlot();
[javac] ^
[javac] class file for org.jfree.ui.Drawable not found
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:102: warning: NotImplementedException is internal proprietary API and may be removed in a future release
[javac] throw new NotImplementedException();
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/igv/igv-2.3.92.ebuild | 87 +++++++++++++++++++++++++++++++++++++++
1 file changed, 87 insertions(+)
diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
new file mode 100644
index 000000000..72b0dcff1
--- /dev/null
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+if [ "$PV" == "9999" ]; then
+ #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+ EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
+ KEYWORDS=""
+ # binaries
+ # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
+ # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
+fi
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="" # see upstream issue #332
+
+# actually more exactly the COMMON_DEPS should contain:
+# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
+COMMON_DEPS="
+ dev-java/absolutelayout:0
+ dev-java/jama:0
+ dev-java/commons-compress
+ dev-java/commons-logging:0
+ >=dev-java/commons-io-2.1:1
+ >=dev-java/commons-math-2:*
+ >=dev-java/commons-jexl-2:*
+ dev-java/jcommon:*
+ >=dev-java/jfreechart-1.0:*
+ dev-java/jlfgr:0
+ dev-java/log4j:0
+ >=dev-java/gson-2.2.2:*
+ =dev-java/guava-17:*
+ >=dev-java/swing-layout-1
+ dev-java/jgrapht:0
+ >=dev-java/junit-4"
+
+DEPEND=">=virtual/jdk-1.7
+ app-arch/unzip
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.7
+ ${COMMON_DEPS}"
+
+S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+EANT_EXTRA_ARGS="-Dnotests=true"
+
+EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
+
+java_prepare() {
+ mv lib oldlib || die
+ mkdir lib || die
+
+ mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
+ mv -v oldlib/batik* lib || die
+
+ rm -rvf oldlib/* || die
+}
+
+src_install() {
+ java-pkg_newjar igv.jar
+
+ for i in lib/*.jar; do java-pkg_dojar $i; done
+
+ java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}
+
+pkg_postinst(){
+ einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
+}
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-11-11 15:11 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-11-11 15:11 UTC (permalink / raw
To: gentoo-commits
commit: c31767db22c797a56e5683b36f07c00adfe11427
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 11 15:10:45 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 11 15:10:45 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c31767db
sci-biology/igv: bump hardcoded version of needed JAR dependency
Package-Manager: portage-2.3.0
sci-biology/igv/igv-2.3.88.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 2a03eac..1f22a4d 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -63,7 +63,7 @@ EANT_NEEDS_TOOLS="true"
EANT_EXTRA_ARGS="-Dnotests=true"
EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
java_prepare() {
mv lib oldlib || die
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-11-08 19:27 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-11-08 19:27 UTC (permalink / raw
To: gentoo-commits
commit: 28e8a88f0ac87bef716fbdb68dcdd52439980236
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 8 19:25:26 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 8 19:25:26 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=28e8a88f
sci-biology/igv: fix DEPS so that ebuild+repoman are happy (but emerge complains)
Package-Manager: portage-2.3.0
sci-biology/igv/igv-2.3.81.ebuild | 18 +++++++++---------
.../igv/{igv-2.3.81.ebuild => igv-2.3.88.ebuild} | 18 +++++++++---------
2 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index 99407f6..b7c3b3d 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -32,22 +32,22 @@ KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.ja
# actually more exactly the COMMON_DEPS should contain:
# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
COMMON_DEPS="
- dev-java/absolutelayout
+ dev-java/absolutelayout:0
dev-java/jama:0
dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
- dev-java/commons-math:2
- dev-java/commons-jexl:2
- dev-java/jcommon:1.0
- dev-java/jfreechart:1.0
+ dev-java/commons-math:*
+ dev-java/commons-jexl:*
+ dev-java/jcommon:*
+ dev-java/jfreechart:*
dev-java/jlfgr:0
dev-java/log4j:0
- dev-java/gson:2.2.2
- dev-java/guava:*
- dev-java/swing-layout:1
+ dev-java/gson:*
+ >=dev-java/guava-17:*
+ dev-java/swing-layout:*
dev-java/jgrapht:0
- dev-java/junit:4"
+ dev-java/junit:0"
DEPEND=">=virtual/jdk-1.7
app-arch/unzip
diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
similarity index 88%
copy from sci-biology/igv/igv-2.3.81.ebuild
copy to sci-biology/igv/igv-2.3.88.ebuild
index 99407f6..2a03eac 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -27,27 +27,27 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
-KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
+KEYWORDS="" # see upstream issue #332
# actually more exactly the COMMON_DEPS should contain:
# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
COMMON_DEPS="
- dev-java/absolutelayout
+ dev-java/absolutelayout:0
dev-java/jama:0
dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
- dev-java/commons-math:2
- dev-java/commons-jexl:2
- dev-java/jcommon:1.0
- dev-java/jfreechart:1.0
+ dev-java/commons-math:*
+ dev-java/commons-jexl:*
+ dev-java/jcommon:*
+ dev-java/jfreechart:*
dev-java/jlfgr:0
dev-java/log4j:0
- dev-java/gson:2.2.2
+ dev-java/gson:*
dev-java/guava:*
- dev-java/swing-layout:1
+ dev-java/swing-layout:*
dev-java/jgrapht:0
- dev-java/junit:4"
+ dev-java/junit:*"
DEPEND=">=virtual/jdk-1.7
app-arch/unzip
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-11-08 18:05 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-11-08 18:05 UTC (permalink / raw
To: gentoo-commits
commit: 238da568a2256a9c3c543723e978efc24d053a3b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 8 18:05:06 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 8 18:05:06 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=238da568
sci-biology/igv: change 'dev-java/guava:17' to 'dev-java/guava:*'
Package-Manager: portage-2.3.0
sci-biology/igv/igv-2.3.47.ebuild | 4 ++--
sci-biology/igv/igv-2.3.81.ebuild | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
index 796421d..e9a7246 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.47.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -41,7 +41,7 @@ COMMON_DEPS="
dev-java/jlfgr:0
dev-java/log4j:0
dev-java/gson:2.2.2
- dev-java/guava:17
+ dev-java/guava:*
dev-java/swing-layout:1
dev-java/jgrapht:0
dev-java/junit:4"
diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index ada8216..99407f6 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -44,7 +44,7 @@ COMMON_DEPS="
dev-java/jlfgr:0
dev-java/log4j:0
dev-java/gson:2.2.2
- dev-java/guava:17
+ dev-java/guava:*
dev-java/swing-layout:1
dev-java/jgrapht:0
dev-java/junit:4"
^ permalink raw reply related [flat|nested] 22+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-09-15 18:36 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-09-15 18:36 UTC (permalink / raw
To: gentoo-commits
commit: 4b20ff857e00c41441df98d719a15c44b52d3b14
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 15 18:35:46 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 15 18:35:46 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b20ff85
sci-biology/igv: version bump, no KEYWORDS
Package-Manager: portage-2.3.0
sci-biology/igv/{igv-2.3.80.ebuild => igv-2.3.81.ebuild} | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
similarity index 87%
rename from sci-biology/igv/igv-2.3.80.ebuild
rename to sci-biology/igv/igv-2.3.81.ebuild
index 033d189..ada8216 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -27,12 +27,14 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
-KEYWORDS=""
+KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
+# actually more exactly the COMMON_DEPS should contain:
+# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
COMMON_DEPS="
dev-java/absolutelayout
dev-java/jama:0
- >=dev-java/commons-compress-1.11
+ dev-java/commons-compress
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
dev-java/commons-math:2
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-08-19 18:47 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-08-19 18:47 UTC (permalink / raw
To: gentoo-commits
commit: 34835e94002d94604c50e66f5fbeb2c42af24966
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:47:02 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:47:02 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34835e94
sci-biology/igv-2.3.80: keep bundled mysql-connector-java-3.1.14-bin.jar
Package-Manager: portage-2.3.0
sci-biology/igv/igv-2.3.80.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
index c4b3128..033d189 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -67,7 +67,7 @@ java_prepare() {
mv lib oldlib || die
mkdir lib || die
- mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+ mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
mv -v oldlib/batik* lib || die
rm -rvf oldlib/* || die
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-08-19 18:21 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-08-19 18:21 UTC (permalink / raw
To: gentoo-commits
commit: ea8d52f984b5df0dfc29312164e9ae2071bed64a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:21:28 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:21:28 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea8d52f9
sci-biology/igv-2.3.80: add dependency on a yet non-existing >=dev-java/commons-compress:1.11 (Gentoo bug #535890)
Package-Manager: portage-2.3.0
sci-biology/igv/igv-2.3.80.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
index 55697a9..c4b3128 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -32,6 +32,7 @@ KEYWORDS=""
COMMON_DEPS="
dev-java/absolutelayout
dev-java/jama:0
+ >=dev-java/commons-compress-1.11
dev-java/commons-logging:0
>=dev-java/commons-io-2.1:1
dev-java/commons-math:2
^ permalink raw reply related [flat|nested] 22+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2016-08-19 18:07 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2016-08-19 18:07 UTC (permalink / raw
To: gentoo-commits
commit: cc5f20a95234b3565df52116900041d251625751
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:07:39 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:07:39 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc5f20a9
sci-biology/igv-2.3.80: version bump, not working yet (upstream github issue #293)
Package-Manager: portage-2.3.0
sci-biology/igv/{igv-2.3.52.ebuild => igv-2.3.80.ebuild} | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/igv/igv-2.3.52.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
similarity index 80%
rename from sci-biology/igv/igv-2.3.52.ebuild
rename to sci-biology/igv/igv-2.3.80.ebuild
index 9318aa4..55697a9 100644
--- a/sci-biology/igv/igv-2.3.52.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -27,7 +27,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64"
+KEYWORDS=""
COMMON_DEPS="
dev-java/absolutelayout
@@ -52,7 +52,7 @@ DEPEND=">=virtual/jdk-1.7
RDEPEND=">=virtual/jre-1.7
${COMMON_DEPS}"
-S="${WORKDIR}/igv-${PV}"
+S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
EANT_BUILD_TARGET="all"
JAVA_ANT_REWRITE_CLASSPATH="true"
@@ -66,12 +66,10 @@ java_prepare() {
mv lib oldlib || die
mkdir lib || die
- mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+ mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
mv -v oldlib/batik* lib || die
rm -rvf oldlib/* || die
-
- epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
}
src_install() {
@@ -81,3 +79,7 @@ src_install() {
java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
}
+
+pkg_postinst(){
+ einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
+}
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 22+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: d719dd2f8a4bccd00e4e3684e695d06511d7919f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:11:33 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:11:33 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d719dd2f
sci-biology/igv: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/igv/ChangeLog | 3 +++
sci-biology/igv/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 20edbae..243b3e9 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/igv: Add github to remote-id in metadata.xml
+
*igv-2.3.52 (11 May 2015)
11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
index fc7c769..ddebe60 100644
--- a/sci-biology/igv/metadata.xml
+++ b/sci-biology/igv/metadata.xml
@@ -6,4 +6,7 @@
<name>Andrey Kislyuk</name>
</maintainer>
<herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="github">broadinstitute/IGV</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-04-29 20:49 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2015-04-29 20:49 UTC (permalink / raw
To: gentoo-commits
commit: a8b5bd66723f0cd98dbab835ca4248e8be7d7b92
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr 29 20:49:16 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 29 20:49:16 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a8b5bd66
sci-biology/igv: version bump
Package-Manager: portage-2.2.18
sci-biology/igv/ChangeLog | 6 ++++++
sci-biology/igv/{igv-2.3.44.ebuild => igv-2.3.47.ebuild} | 0
2 files changed, 6 insertions(+)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 57365d0..8198c3c 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*igv-2.3.47 (29 Apr 2015)
+
+ 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.47.ebuild,
+ -igv-2.3.44.ebuild:
+ sci-biology/igv: version bump
+
21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild:
Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as
requested by Martin Mokrejŝ (note: i've excluded the test code by passing
diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
similarity index 100%
rename from sci-biology/igv/igv-2.3.44.ebuild
rename to sci-biology/igv/igv-2.3.47.ebuild
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-03-23 8:10 Justin Lecher
0 siblings, 0 replies; 22+ messages in thread
From: Justin Lecher @ 2015-03-23 8:10 UTC (permalink / raw
To: gentoo-commits
commit: b63f594da84935c8eb06d4102b8724f621c5e4fe
Author: Johann Schmitz <johann <AT> j-schmitz <DOT> net>
AuthorDate: Sat Mar 21 17:33:30 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 21 17:33:30 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b63f594d
Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as requested by Martin Mokrejŝ (note: i've excluded the test code by passing -Dnotests=true to ant so it may break at some point).
Also improved the ebuild by unbundling stuff we already have in portage. There are quite a number of libraries which aren't used for compilation which may be needed at runtime. I haven't tested the program in depth: it started at didn't throw errors when i clicked around - everything else is way beyond my knowledge.
Improved the ebuild for sci-biology/igv
Package-Manager: portage-2.2.14
sci-biology/igv/ChangeLog | 10 ++++
sci-biology/igv/igv-2.3.44.ebuild | 109 +++++++++++++-------------------------
2 files changed, 48 insertions(+), 71 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 80d76fd..9eb94ff 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,16 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild:
+ Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as
+ requested by Martin Mokrejŝ (note: i've excluded the test code by passing
+ -Dnotests=true to ant so it may break at some point). Also improved the
+ ebuild by unbundling stuff we already have in portage. There are quite a
+ number of libraries which aren't used for compilation which may be needed at
+ runtime. I haven't tested the program in depth: it started at didn't throw
+ errors when i clicked around - everything else is way beyond my knowledge.
+ Improved the ebuild for sci-biology/igv
+
17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
fix inherit to use git instead of previously used subversion
diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index f14d511..1464033 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -14,18 +14,13 @@ if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
KEYWORDS=""
else
- SRC_URI="https://github.com/broadinstitute/IGV/archive/v"${PV}".zip"
+ SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
KEYWORDS=""
# binaries
# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
fi
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-WANT_ANT_TASKS="ant-apache-bcel"
-
DESCRIPTION="Integrative Genomics Viewer"
HOMEPAGE="http://www.broadinstitute.org/igv/"
@@ -35,79 +30,51 @@ IUSE=""
KEYWORDS="~amd64"
COMMON_DEPS="
- dev-java/batik
dev-java/absolutelayout
- dev-java/jama
- dev-java/commons-logging
- dev-java/commons-math:3
- dev-java/concurrent-util
- dev-java/jcommon
- dev-java/jfreechart
- dev-java/hdf-java
- dev-java/jlfgr
- dev-java/junit:0
- dev-java/log4j
- dev-db/mysql-connector-c++
- sci-biology/samtools
- dev-java/swing-layout
- sci-biology/vcftools"
-DEPEND=">=virtual/jdk-1.6:*
+ dev-java/jama:0
+ dev-java/commons-logging:0
+ >=dev-java/commons-io-2.1:1
+ dev-java/commons-math:2
+ dev-java/commons-jexl:2
+ dev-java/jcommon:1.0
+ dev-java/jfreechart:1.0
+ dev-java/jlfgr:0
+ dev-java/log4j:0
+ dev-java/gson:2.2.2
+ dev-java/guava:17
+ dev-java/swing-layout:1
+ dev-java/jgrapht:0
+ dev-java/junit:4"
+
+DEPEND=">=virtual/jdk-1.7
+ app-arch/unzip
${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6:*
+RDEPEND=">=virtual/jre-1.7
${COMMON_DEPS}"
-S="${WORKDIR}"/IGV-"${PV}"
+S="${WORKDIR}/IGV-${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+EANT_EXTRA_ARGS="-Dnotests=true"
+
+EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+
+java_prepare() {
+ mv lib oldlib || die
+ mkdir lib || die
+
+ mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+ mv -v oldlib/batik* lib || die
+
+ rm -rvf oldlib/* || die
+}
src_install() {
java-pkg_newjar igv.jar
- # probably could drop some of these below
- #
- # /usr/share/igv/lib/AbsoluteLayout.jar
- # /usr/share/igv/lib/Jama-1.0.2.jar
- # /usr/share/igv/lib/batik-awt-util.jar
- # /usr/share/igv/lib/batik-bridge.jar
- # /usr/share/igv/lib/batik-codec.jar
- # /usr/share/igv/lib/batik-css.jar
- # /usr/share/igv/lib/batik-dom.jar
- # /usr/share/igv/lib/batik-ext.jar
- # /usr/share/igv/lib/batik-gui-util.jar
- # /usr/share/igv/lib/batik-gvt.jar
- # /usr/share/igv/lib/batik-parser.jar
- # /usr/share/igv/lib/batik-svg-dom.jar
- # /usr/share/igv/lib/batik-svggen.jar
- # /usr/share/igv/lib/batik-transcoder.jar
- # /usr/share/igv/lib/batik-util.jar
- # /usr/share/igv/lib/batik-xml.jar
- # /usr/share/igv/lib/commons-logging-1.1.1.jar
- # /usr/share/igv/lib/commons-math-1.1.jar
- # /usr/share/igv/lib/concurrent.jar
- # /usr/share/igv/lib/goby-io-igv.jar
- # /usr/share/igv/lib/igv.jar
- # /usr/share/igv/lib/jargs.jar
- # /usr/share/igv/lib/jcommon-1.0.16.jar
- # /usr/share/igv/lib/jfreechart-1.0.13.jar
- # /usr/share/igv/lib/jhdf.jar
- # /usr/share/igv/lib/jhdf5.jar
- # /usr/share/igv/lib/jide-action.jar
- # /usr/share/igv/lib/jide-common.jar
- # /usr/share/igv/lib/jide-components.jar
- # /usr/share/igv/lib/jide-dialogs.jar
- # /usr/share/igv/lib/jide-dock.jar
- # /usr/share/igv/lib/jide-grids.jar
- # /usr/share/igv/lib/jlfgr-1_0.jar
- # /usr/share/igv/lib/junit-4.5.jar
- # /usr/share/igv/lib/log4j-1.2.15.jar
- # /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar
- # /usr/share/igv/lib/sam-1.53.jar
- # /usr/share/igv/lib/swing-layout-1.0.jar
- # /usr/share/igv/lib/vcf.jar
- # /usr/share/igv/lib/xml-apis-1.3.04.jar
- # /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
- cd lib || die
- rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die
- cd .. || die
-
for i in lib/*.jar; do java-pkg_dojar $i; done
java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-03-21 1:20 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2015-03-21 1:20 UTC (permalink / raw
To: gentoo-commits
commit: 3f16f13abbf30d2dbcec009316baca0bbed457ee
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 21 01:19:28 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 21 01:19:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f16f13a
sci-biology/igv: fix inherit to git-r3
Package-Manager: portage-2.2.15
sci-biology/igv/ChangeLog | 3 +++
sci-biology/igv/igv-2.3.44.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 80d76fd..bb4f3a0 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
+ sci-biology/igv: fix inherit to git-r3
+
17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
fix inherit to use git instead of previously used subversion
diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index f14d511..5b6554a 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-[ "$PV" == "9999" ] && inherit git-3
+[ "$PV" == "9999" ] && inherit git-r3
if [ "$PV" == "9999" ]; then
#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
^ permalink raw reply related [flat|nested] 22+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-03-17 19:24 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2015-03-17 19:24 UTC (permalink / raw
To: gentoo-commits
commit: c141fec70ce878a899f15d93a676ec997a19c44a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 19:23:52 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 19:23:52 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c141fec7
fix inherit to use git instead of previously used subversion
Package-Manager: portage-2.2.15
sci-biology/igv/ChangeLog | 3 +++
sci-biology/igv/igv-2.3.44.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 9550c7e..80d76fd 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
+ fix inherit to use git instead of previously used subversion
+
*igv-2.3.44 (17 Mar 2015)
17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild,
diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index 3ed561b..f14d511 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-[ "$PV" == "9999" ] && inherit subversion
+[ "$PV" == "9999" ] && inherit git-3
if [ "$PV" == "9999" ]; then
#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
^ permalink raw reply related [flat|nested] 22+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-03-17 12:14 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2015-03-17 12:14 UTC (permalink / raw
To: gentoo-commits
commit: dee2b1bbe26a162de955226a1f8c758079bd5680
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 12:13:13 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 12:13:13 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dee2b1bb
version bump
Package-Manager: portage-2.2.15
sci-biology/igv/ChangeLog | 6 ++++++
sci-biology/igv/{igv-2.3.40.ebuild => igv-2.3.44.ebuild} | 0
2 files changed, 6 insertions(+)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 457a903..9550c7e 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*igv-2.3.44 (17 Mar 2015)
+
+ 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild,
+ -igv-2.3.40.ebuild:
+ version bump
+
*igv-2.3.40 (05 Mar 2015)
05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild,
diff --git a/sci-biology/igv/igv-2.3.40.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
similarity index 100%
rename from sci-biology/igv/igv-2.3.40.ebuild
rename to sci-biology/igv/igv-2.3.44.ebuild
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2015-03-05 9:52 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2015-03-05 9:52 UTC (permalink / raw
To: gentoo-commits
commit: 73e1b2f7e9caa1684ab9c9dc8f778523fc7e1c8c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 5 09:52:13 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 5 09:52:13 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=73e1b2f7
updated ebuild to github URLs; version bump but does not compile for me
Package-Manager: portage-2.2.15
sci-biology/igv/ChangeLog | 6 ++++++
.../igv/{igv-2.0.35.ebuild => igv-2.3.40.ebuild} | 25 ++++++++++++++++------
2 files changed, 25 insertions(+), 6 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 8fe0e05..457a903 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*igv-2.3.40 (05 Mar 2015)
+
+ 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild,
+ -igv-2.0.35.ebuild:
+ updated ebuild to github URLs; version bump but does not compile for me
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild,
igv-2.0.35.ebuild, metadata.xml:
sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds
diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.3.40.ebuild
similarity index 82%
rename from sci-biology/igv/igv-2.0.35.ebuild
rename to sci-biology/igv/igv-2.3.40.ebuild
index e5d4e93..3ed561b 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.3.40.ebuild
@@ -4,24 +4,35 @@
EAPI=5
-#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit subversion
+
+if [ "$PV" == "9999" ]; then
+ #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+ EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/broadinstitute/IGV/archive/v"${PV}".zip"
+ KEYWORDS=""
+ # binaries
+ # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
+ # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
+fi
EANT_BUILD_TARGET="all"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_NEEDS_TOOLS="true"
WANT_ANT_TASKS="ant-apache-bcel"
-inherit subversion java-pkg-2 java-ant-2
-
DESCRIPTION="Integrative Genomics Viewer"
HOMEPAGE="http://www.broadinstitute.org/igv/"
-SRC_URI=""
LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
-KEYWORDS=""
+KEYWORDS="~amd64"
COMMON_DEPS="
dev-java/batik
@@ -45,6 +56,8 @@ DEPEND=">=virtual/jdk-1.6:*
RDEPEND=">=virtual/jre-1.6:*
${COMMON_DEPS}"
+S="${WORKDIR}"/IGV-"${PV}"
+
src_install() {
java-pkg_newjar igv.jar
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2014-03-23 23:37 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2014-03-23 23:37 UTC (permalink / raw
To: gentoo-commits
commit: ece4e92e9c754626484b6ff0d499a1ce6189e2b0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:36:44 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:36:44 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ece4e92e
API bumped, whitespace removal
Package-Manager: portage-2.2.7
---
sci-biology/igv/ChangeLog | 3 +++
sci-biology/igv/igv-2.0.35.ebuild | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index dec3275..57895e3 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
+ API bumped, whitespace removal
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
added some dev-java dependencies and removed some bundled .jar files
*igv-2.0.35 (23 Mar 2014)
diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index 457e8c8..a9021e7 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
@@ -92,7 +92,7 @@ src_install() {
cd lib || die
rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
cd ..
-
+
for i in lib/*.jar; do java-pkg_dojar $i; done
java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2014-03-23 23:33 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2014-03-23 23:33 UTC (permalink / raw
To: gentoo-commits
commit: 9cb4024ef4caa9586b3ba4f1f73851a7dd449ddf
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:32:00 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:32:00 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cb4024e
added some dev-java dependencies and removed some bundled .jar files
Package-Manager: portage-2.2.7
---
sci-biology/igv/ChangeLog | 3 ++
sci-biology/igv/igv-2.0.35.ebuild | 66 ++++++++++++++++++++++++++++++++++++++-
2 files changed, 68 insertions(+), 1 deletion(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index de4a770..dec3275 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
+ added some dev-java dependencies and removed some bundled .jar files
+
*igv-2.0.35 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.0.35.ebuild:
diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index 67a0c5b..457e8c8 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -22,7 +22,22 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64"
-COMMON_DEPS=""
+COMMON_DEPS="dev-java/batik
+ dev-java/absolutelayout
+ dev-java/jama
+ dev-java/commons-logging
+ dev-java/commons-math
+ dev-java/concurrent-util
+ dev-java/jcommon
+ dev-java/jfreechart
+ dev-java/hdf-java
+ dev-java/jlfgr
+ dev-java/junit
+ dev-java/log4j
+ dev-db/mysql-connector-c++
+ sci-biology/samtools
+ dev-java/swing-layout
+ sci-biology/vcftools"
DEPEND=">=virtual/jdk-1.6
${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.6
@@ -30,6 +45,55 @@ RDEPEND=">=virtual/jre-1.6
src_install() {
java-pkg_newjar igv.jar
+
+ # probably could drop some of these below
+ #
+ # /usr/share/igv/lib/AbsoluteLayout.jar
+ # /usr/share/igv/lib/Jama-1.0.2.jar
+ # /usr/share/igv/lib/batik-awt-util.jar
+ # /usr/share/igv/lib/batik-bridge.jar
+ # /usr/share/igv/lib/batik-codec.jar
+ # /usr/share/igv/lib/batik-css.jar
+ # /usr/share/igv/lib/batik-dom.jar
+ # /usr/share/igv/lib/batik-ext.jar
+ # /usr/share/igv/lib/batik-gui-util.jar
+ # /usr/share/igv/lib/batik-gvt.jar
+ # /usr/share/igv/lib/batik-parser.jar
+ # /usr/share/igv/lib/batik-svg-dom.jar
+ # /usr/share/igv/lib/batik-svggen.jar
+ # /usr/share/igv/lib/batik-transcoder.jar
+ # /usr/share/igv/lib/batik-util.jar
+ # /usr/share/igv/lib/batik-xml.jar
+ # /usr/share/igv/lib/commons-logging-1.1.1.jar
+ # /usr/share/igv/lib/commons-math-1.1.jar
+ # /usr/share/igv/lib/concurrent.jar
+ # /usr/share/igv/lib/goby-io-igv.jar
+ # /usr/share/igv/lib/igv.jar
+ # /usr/share/igv/lib/jargs.jar
+ # /usr/share/igv/lib/jcommon-1.0.16.jar
+ # /usr/share/igv/lib/jfreechart-1.0.13.jar
+ # /usr/share/igv/lib/jhdf.jar
+ # /usr/share/igv/lib/jhdf5.jar
+ # /usr/share/igv/lib/jide-action.jar
+ # /usr/share/igv/lib/jide-common.jar
+ # /usr/share/igv/lib/jide-components.jar
+ # /usr/share/igv/lib/jide-dialogs.jar
+ # /usr/share/igv/lib/jide-dock.jar
+ # /usr/share/igv/lib/jide-grids.jar
+ # /usr/share/igv/lib/jlfgr-1_0.jar
+ # /usr/share/igv/lib/junit-4.5.jar
+ # /usr/share/igv/lib/log4j-1.2.15.jar
+ # /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar
+ # /usr/share/igv/lib/sam-1.53.jar
+ # /usr/share/igv/lib/swing-layout-1.0.jar
+ # /usr/share/igv/lib/vcf.jar
+ # /usr/share/igv/lib/xml-apis-1.3.04.jar
+ # /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
+ cd lib || die
+ rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
+ cd ..
+
for i in lib/*.jar; do java-pkg_dojar $i; done
+
java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
}
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2014-03-23 23:00 Martin Mokrejs
0 siblings, 0 replies; 22+ messages in thread
From: Martin Mokrejs @ 2014-03-23 23:00 UTC (permalink / raw
To: gentoo-commits
commit: 0da34aea17b8bc8a2d2f088acb0296dcfdd6b923
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 22:59:12 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 22:59:12 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0da34aea
sci-biology/igv-2.0.35: version bump
Package-Manager: portage-2.2.7
---
sci-biology/igv/ChangeLog | 8 ++++++--
sci-biology/igv/igv-2.0.35.ebuild | 35 +++++++++++++++++++++++++++++++++++
2 files changed, 41 insertions(+), 2 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 69f3a962..de4a770 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/igv
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*igv-2.0.35 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.0.35.ebuild:
+ sci-biology/igv-2.0.35: version bump
+
08 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
New package, ebuild written by me
-
diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
new file mode 100644
index 0000000..67a0c5b
--- /dev/null
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+WANT_ANT_TASKS="ant-apache-bcel"
+
+inherit subversion java-pkg-2 java-ant-2
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+SRC_URI=""
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}"
+
+src_install() {
+ java-pkg_newjar igv.jar
+ for i in lib/*.jar; do java-pkg_dojar $i; done
+ java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}
^ permalink raw reply related [flat|nested] 22+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
@ 2012-01-08 8:10 Andrey Kislyuk
0 siblings, 0 replies; 22+ messages in thread
From: Andrey Kislyuk @ 2012-01-08 8:10 UTC (permalink / raw
To: gentoo-commits
commit: f232fc33ddad7f0e36961486a4c6125a62feae29
Author: Andrey Kislyuk <kislyuk <AT> gmail <DOT> com>
AuthorDate: Sun Jan 8 08:10:22 2012 +0000
Commit: Andrey Kislyuk <weaver <AT> gentoo <DOT> org>
CommitDate: Sun Jan 8 08:10:22 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f232fc33
New package, ebuild written by me
---
sci-biology/igv/ChangeLog | 7 +++++++
sci-biology/igv/igv-2.0.32.ebuild | 35 +++++++++++++++++++++++++++++++++++
sci-biology/igv/metadata.xml | 9 +++++++++
3 files changed, 51 insertions(+), 0 deletions(-)
diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
new file mode 100644
index 0000000..69f3a962
--- /dev/null
+++ b/sci-biology/igv/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/igv
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 08 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+ New package, ebuild written by me
+
diff --git a/sci-biology/igv/igv-2.0.32.ebuild b/sci-biology/igv/igv-2.0.32.ebuild
new file mode 100644
index 0000000..ef2dc7f
--- /dev/null
+++ b/sci-biology/igv/igv-2.0.32.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+WANT_ANT_TASKS="ant-apache-bcel"
+
+inherit subversion java-pkg-2 java-ant-2
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+SRC_URI=""
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}"
+
+src_install() {
+ java-pkg_newjar igv.jar
+ for i in lib/*.jar; do java-pkg_dojar $i; done
+ java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}
diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
new file mode 100644
index 0000000..3302123
--- /dev/null
+++ b/sci-biology/igv/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 22+ messages in thread
end of thread, other threads:[~2017-04-06 22:57 UTC | newest]
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