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

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

[Martin Mokrejs]

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"

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

[Christoph Junghans]

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"
 

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

[Martin Mokrejs]

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
+}

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

[Martin Mokrejs]

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>

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

[Martin Mokrejs]

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>

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

[Martin Mokrejs]

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
+}

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

[Martin Mokrejs]

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
+}

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

[Martin Mokrejs]

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
 

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

[Andrew Ammerlaan]

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:*

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

[Andrew Ammerlaan]

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