* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2016-11-15 18:32 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-11-15 18:32 UTC (permalink / raw
To: gentoo-commits
commit: 6911112e32296b390cdd2bda69aba1ae426a2031
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Nov 14 23:08:02 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Nov 14 23:08:02 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6911112e
sci-biology/VarScan: remove a package skeleton, no sources available
sci-biology/VarScan/VarScan-2.3.7.ebuild | 30 ------------------------------
sci-biology/VarScan/metadata.xml | 11 -----------
2 files changed, 41 deletions(-)
diff --git a/sci-biology/VarScan/VarScan-2.3.7.ebuild b/sci-biology/VarScan/VarScan-2.3.7.ebuild
deleted file mode 100644
index f1b31c7..0000000
--- a/sci-biology/VarScan/VarScan-2.3.7.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls"
-HOMEPAGE="http://varscan.sourceforge.net/"
-
-# binary
-#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
-#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
-SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- >=virtual/jdk-1.5:*"
-RDEPEND=">=virtual/jre-1.5:*"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_compile(){
- javac *.java
-}
diff --git a/sci-biology/VarScan/metadata.xml b/sci-biology/VarScan/metadata.xml
deleted file mode 100644
index fae01f1..0000000
--- a/sci-biology/VarScan/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">varscan</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2023-02-10 13:52 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2023-02-10 13:52 UTC (permalink / raw
To: gentoo-commits
commit: f4b2c7a728089bb8932a2fb5ea509e2326f5a63e
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 10 13:51:44 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 10 13:51:44 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f4b2c7a7
sci-biology/VarScan: fix misplaced weak blocker
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/VarScan/VarScan-2.4.4.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/VarScan/VarScan-2.4.4.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild
index 72a3c94df..039a68f06 100644
--- a/sci-biology/VarScan/VarScan-2.4.4.ebuild
+++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild
@@ -18,9 +18,11 @@ KEYWORDS="~amd64"
DEPEND="
>=virtual/jdk-1.5:*
- !sci-biology/VarScan-bin"
+"
RDEPEND=">=virtual/jre-1.5:*
- sci-biology/bam-readcount"
+ sci-biology/bam-readcount
+ !sci-biology/VarScan-bin
+"
S="${WORKDIR}"/net/sf/varscan
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2021-03-05 18:39 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2021-03-05 18:39 UTC (permalink / raw
To: gentoo-commits
commit: cbd0aa94ac67bb0371412b7dd392ae89fba4f6bd
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar 5 18:36:36 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar 5 18:36:36 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbd0aa94
sci-biology/VarScan: EAPI bump, vers bump, fix fetch
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/VarScan/VarScan-2.4.2.ebuild | 36 ----------------------
.../{VarScan-2.4.3.ebuild => VarScan-2.4.4.ebuild} | 7 ++---
2 files changed, 3 insertions(+), 40 deletions(-)
diff --git a/sci-biology/VarScan/VarScan-2.4.2.ebuild b/sci-biology/VarScan/VarScan-2.4.2.ebuild
deleted file mode 100644
index 4add5f679..000000000
--- a/sci-biology/VarScan/VarScan-2.4.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
-HOMEPAGE="http://varscan.sourceforge.net/"
-
-# binary
-#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
-#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
-SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
- >=virtual/jdk-1.5:*
- !sci-biology/VarScan-bin"
-RDEPEND=">=virtual/jre-1.5:*
- sci-biology/bam-readcount"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_compile(){
- javac *.java
-}
-
-src_install(){
- java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
- java-pkg_dolauncher VarScan
-}
diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild
similarity index 86%
rename from sci-biology/VarScan/VarScan-2.4.3.ebuild
rename to sci-biology/VarScan/VarScan-2.4.4.ebuild
index 0b3fc2ad5..72a3c94df 100644
--- a/sci-biology/VarScan/VarScan-2.4.3.ebuild
+++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit java-pkg-2
@@ -10,12 +10,11 @@ HOMEPAGE="http://varscan.sourceforge.net/"
# binary
#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar
-SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
+SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v${PV}.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
LICENSE="Non-profit-OSL-3.0"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
DEPEND="
>=virtual/jdk-1.5:*
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2017-04-14 17:17 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-04-14 17:17 UTC (permalink / raw
To: gentoo-commits
commit: 2ddeb5981f5bbc80372aec79547a739ef1b1245f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 14 17:17:20 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 14 17:17:20 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ddeb598
sci-biology/VarScan: add RDEPEND on bam-readcount
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/VarScan/VarScan-2.4.2.ebuild | 5 +++--
sci-biology/VarScan/VarScan-2.4.3.ebuild | 3 ++-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/VarScan/VarScan-2.4.2.ebuild b/sci-biology/VarScan/VarScan-2.4.2.ebuild
index 36af35941..4add5f679 100644
--- a/sci-biology/VarScan/VarScan-2.4.2.ebuild
+++ b/sci-biology/VarScan/VarScan-2.4.2.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
EAPI=5
@@ -21,7 +21,8 @@ IUSE=""
DEPEND="
>=virtual/jdk-1.5:*
!sci-biology/VarScan-bin"
-RDEPEND=">=virtual/jre-1.5:*"
+RDEPEND=">=virtual/jre-1.5:*
+ sci-biology/bam-readcount"
S="${WORKDIR}"/net/sf/varscan
diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.3.ebuild
index 8c42848c1..0b3fc2ad5 100644
--- a/sci-biology/VarScan/VarScan-2.4.3.ebuild
+++ b/sci-biology/VarScan/VarScan-2.4.3.ebuild
@@ -20,7 +20,8 @@ IUSE=""
DEPEND="
>=virtual/jdk-1.5:*
!sci-biology/VarScan-bin"
-RDEPEND=">=virtual/jre-1.5:*"
+RDEPEND=">=virtual/jre-1.5:*
+ sci-biology/bam-readcount"
S="${WORKDIR}"/net/sf/varscan
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2017-02-20 18:51 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-02-20 18:51 UTC (permalink / raw
To: gentoo-commits
commit: da001fc52d309509f4bc99d41b8b147672e8ac33
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 18:51:04 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 18:51:04 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=da001fc5
sci-biology/VarScan: version bump
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/VarScan/VarScan-2.4.3.ebuild | 35 ++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.3.ebuild
new file mode 100644
index 000000000..3ef29a10c
--- /dev/null
+++ b/sci-biology/VarScan/VarScan-2.4.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
+HOMEPAGE="http://varscan.sourceforge.net/"
+
+# binary
+#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar
+SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ >=virtual/jdk-1.5:*
+ !sci-biology/VarScan-bin"
+RDEPEND=">=virtual/jre-1.5:*"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_compile(){
+ javac *.java
+}
+
+src_install(){
+ java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
+ java-pkg_dolauncher VarScan
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2016-11-15 19:13 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-11-15 19:13 UTC (permalink / raw
To: gentoo-commits
commit: bee1add2f405f7e728e35c473d6cc85acd05e0e6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 15 19:13:13 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 15 19:13:13 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bee1add2
sci-biology/VarScan: install upstream jar with *.java and *.class files
Package-Manager: portage-2.3.2
.../VarScan/{VarScan-2.3.7.ebuild => VarScan-2.4.2.ebuild} | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/sci-biology/VarScan/VarScan-2.3.7.ebuild b/sci-biology/VarScan/VarScan-2.4.2.ebuild
similarity index 70%
rename from sci-biology/VarScan/VarScan-2.3.7.ebuild
rename to sci-biology/VarScan/VarScan-2.4.2.ebuild
index f1b31c7..63eb84a 100644
--- a/sci-biology/VarScan/VarScan-2.3.7.ebuild
+++ b/sci-biology/VarScan/VarScan-2.4.2.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
# $Id$
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls"
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
HOMEPAGE="http://varscan.sourceforge.net/"
# binary
@@ -16,11 +16,12 @@ SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.ja
LICENSE="Non-profit-OSL-3.0"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND="
- >=virtual/jdk-1.5:*"
+ >=virtual/jdk-1.5:*
+ !sci-biology/VarScan-bin"
RDEPEND=">=virtual/jre-1.5:*"
S="${WORKDIR}"/net/sf/varscan
@@ -28,3 +29,8 @@ S="${WORKDIR}"/net/sf/varscan
src_compile(){
javac *.java
}
+
+src_install(){
+ java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
+ java-pkg_dolauncher VarScan
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2016-11-15 19:05 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-11-15 19:05 UTC (permalink / raw
To: gentoo-commits
commit: e0ff471d76529dece393c722b8fe23753a11a385
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 15 19:05:02 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 15 19:05:02 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0ff471d
Revert "sci-biology/VarScan: remove a package skeleton, no sources available"
This reverts commit 6911112e32296b390cdd2bda69aba1ae426a2031.
sci-biology/VarScan/VarScan-2.3.7.ebuild | 30 ++++++++++++++++++++++++++++++
sci-biology/VarScan/metadata.xml | 11 +++++++++++
2 files changed, 41 insertions(+)
diff --git a/sci-biology/VarScan/VarScan-2.3.7.ebuild b/sci-biology/VarScan/VarScan-2.3.7.ebuild
new file mode 100644
index 0000000..f1b31c7
--- /dev/null
+++ b/sci-biology/VarScan/VarScan-2.3.7.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls"
+HOMEPAGE="http://varscan.sourceforge.net/"
+
+# binary
+#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
+#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
+SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ >=virtual/jdk-1.5:*"
+RDEPEND=">=virtual/jre-1.5:*"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_compile(){
+ javac *.java
+}
diff --git a/sci-biology/VarScan/metadata.xml b/sci-biology/VarScan/metadata.xml
new file mode 100644
index 0000000..fae01f1
--- /dev/null
+++ b/sci-biology/VarScan/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">varscan</remote-id>
+ </upstream>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2015-03-13 12:29 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-03-13 12:29 UTC (permalink / raw
To: gentoo-commits
commit: 790ca1f9862fd92d6a0edc5068e3ae0779d24e55
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 13 12:28:31 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 13 12:28:31 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=790ca1f9
fix SRC_URI to fetch real source code, ebuild improvements but not working
Package-Manager: portage-2.2.15
sci-biology/VarScan/ChangeLog | 6 ++++++
.../{VarScan-2.3.6.ebuild => VarScan-2.3.7.ebuild} | 15 ++++++++++++---
2 files changed, 18 insertions(+), 3 deletions(-)
diff --git a/sci-biology/VarScan/ChangeLog b/sci-biology/VarScan/ChangeLog
index bfcfc5c..a7470a6 100644
--- a/sci-biology/VarScan/ChangeLog
+++ b/sci-biology/VarScan/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*VarScan-2.3.7 (13 Mar 2015)
+
+ 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +VarScan-2.3.7.ebuild, -VarScan-2.3.6.ebuild:
+ fix SRC_URI to fetch real source code, ebuild improvements but not working
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> VarScan-2.3.6.ebuild,
metadata.xml:
sci-biology/VarScan: fix SLOT operators
diff --git a/sci-biology/VarScan/VarScan-2.3.6.ebuild b/sci-biology/VarScan/VarScan-2.3.7.ebuild
similarity index 64%
rename from sci-biology/VarScan/VarScan-2.3.6.ebuild
rename to sci-biology/VarScan/VarScan-2.3.7.ebuild
index a9a9a07..ad7eaa8 100644
--- a/sci-biology/VarScan/VarScan-2.3.6.ebuild
+++ b/sci-biology/VarScan/VarScan-2.3.7.ebuild
@@ -8,7 +8,11 @@ inherit java-pkg-2
DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls"
HOMEPAGE="http://varscan.sourceforge.net/"
-SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
+
+# binary
+#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
+#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
+SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar"
LICENSE="Non-profit-OSL-3.0"
SLOT="0"
@@ -16,6 +20,11 @@ KEYWORDS=""
IUSE=""
DEPEND="
- >=virtual/jdk-1.5:*
- dev-java/ant-core"
+ >=virtual/jdk-1.5:*"
RDEPEND=">=virtual/jre-1.5:*"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_compile(){
+ javac *.java
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2014-09-16 17:50 Christoph Junghans
0 siblings, 0 replies; 10+ messages in thread
From: Christoph Junghans @ 2014-09-16 17:50 UTC (permalink / raw
To: gentoo-commits
commit: c408e91c8e3f2405ab179bf774698ea6456ac5a0
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 17:25:13 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 17:25:13 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c408e91c
fixed DESCRIPTION
Package-Manager: portage-2.2.8-r1
---
sci-biology/VarScan/ChangeLog | 6 ++++++
sci-biology/VarScan/VarScan-2.3.6.ebuild | 2 +-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/VarScan/ChangeLog b/sci-biology/VarScan/ChangeLog
new file mode 100644
index 0000000..b2fcc88
--- /dev/null
+++ b/sci-biology/VarScan/ChangeLog
@@ -0,0 +1,6 @@
+# ChangeLog for sci-biology/VarScan
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> VarScan-2.3.6.ebuild:
+ fixed DESCRIPTION
diff --git a/sci-biology/VarScan/VarScan-2.3.6.ebuild b/sci-biology/VarScan/VarScan-2.3.6.ebuild
index 1051f71..16066ce 100644
--- a/sci-biology/VarScan/VarScan-2.3.6.ebuild
+++ b/sci-biology/VarScan/VarScan-2.3.6.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, somatic copy number alterations (CNA)), SNP calls"
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls"
HOMEPAGE="http://varscan.sourceforge.net/"
SRC_URI="http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VarScan/
@ 2014-03-23 18:26 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 18:26 UTC (permalink / raw
To: gentoo-commits
commit: e26cb1509794089cfcaf22cbead79430ad10cbcc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 18:25:19 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 18:25:19 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e26cb150
sci-biology/VarScan: a new package with some classes and no INSTALL docs, needs help from java team for sure
---
sci-biology/VarScan/VarScan-2.3.6.ebuild | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/sci-biology/VarScan/VarScan-2.3.6.ebuild b/sci-biology/VarScan/VarScan-2.3.6.ebuild
new file mode 100644
index 0000000..1051f71
--- /dev/null
+++ b/sci-biology/VarScan/VarScan-2.3.6.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, somatic copy number alterations (CNA)), SNP calls"
+HOMEPAGE="http://varscan.sourceforge.net/"
+SRC_URI="http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ >=virtual/jdk-1.5
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.5"
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