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

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

[Martin Mokrejs]

commit:     7926b6f0844083f7e9c3976c00cdf61ebebcf501
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun May 10 17:24:18 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun May 10 17:24:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7926b6f0

sci-biology/beagle: a skeleton for a new java package with just *.java files provided

Package-Manager: portage-2.2.18

 sci-biology/beagle/ChangeLog         | 10 ++++++++++
 sci-biology/beagle/beagle-4.0.ebuild | 24 ++++++++++++++++++++++++
 sci-biology/beagle/metadata.xml      |  9 +++++++++
 3 files changed, 43 insertions(+)

diff --git a/sci-biology/beagle/ChangeLog b/sci-biology/beagle/ChangeLog
new file mode 100644
index 0000000..99f4578
--- /dev/null
+++ b/sci-biology/beagle/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/beagle
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*beagle-4.0 (10 May 2015)
+
+  10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +beagle-4.0.ebuild,
+  +metadata.xml:
+  sci-biology/beagle: a skeleton for a new java package with just *.java files
+  provided

diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild
new file mode 100644
index 0000000..9652198
--- /dev/null
+++ b/sci-biology/beagle/beagle-4.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Genotype calling, genotype phasing, imputation of ungenotyped markers, identity-by-descent segment detection"
+HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html"
+SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip
+	http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf
+	http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example -> ${PN}-example.sh
+	http://faculty.washington.edu/browning/beagle/release_notes -> ${PN}-release_notes.txt"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND="${DEPEND}
+	>=virtual/jdk-1.7
+	sci-biology/conform-gt"

diff --git a/sci-biology/beagle/metadata.xml b/sci-biology/beagle/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/beagle/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

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

[Justin Lecher]

commit:     411961b34c67bafc257fb4715773a9103510ecd8
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Sep  4 09:33:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep  4 09:33:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=411961b3

sci-biology/beagle: Fix dependencies and slotting

Package-Manager: portage-2.2.20.1

 sci-biology/beagle/ChangeLog         | 3 +++
 sci-biology/beagle/beagle-4.0.ebuild | 3 +--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/beagle/ChangeLog b/sci-biology/beagle/ChangeLog
index e9d9a7a..16542b7 100644
--- a/sci-biology/beagle/ChangeLog
+++ b/sci-biology/beagle/ChangeLog
@@ -3,6 +3,9 @@
 # $Id$
 
   04 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> beagle-4.0.ebuild:
+  sci-biology/beagle: Fix dependencies and slotting
+
+  04 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> beagle-4.0.ebuild:
   sci-biology/beagle: Adjust too long DESCRIPTION
 
 *beagle-4.0 (10 May 2015)

diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild
index 4686478..70caec7 100644
--- a/sci-biology/beagle/beagle-4.0.ebuild
+++ b/sci-biology/beagle/beagle-4.0.ebuild
@@ -18,7 +18,6 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=">=virtual/jdk-1.7"
+DEPEND=">=virtual/jdk-1.7:*"
 RDEPEND="${DEPEND}
-	>=virtual/jdk-1.7
 	sci-biology/conform-gt"

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

[Justin Lecher]

commit:     af2c83a9eefb99c9862483bf655492dd818ad83c
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Sep  4 09:28:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep  4 09:33:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=af2c83a9

sci-biology/beagle: Adjust too long DESCRIPTION

Package-Manager: portage-2.2.20.1

 sci-biology/beagle/ChangeLog         | 3 +++
 sci-biology/beagle/beagle-4.0.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/beagle/ChangeLog b/sci-biology/beagle/ChangeLog
index 25d9841..e9d9a7a 100644
--- a/sci-biology/beagle/ChangeLog
+++ b/sci-biology/beagle/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  04 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> beagle-4.0.ebuild:
+  sci-biology/beagle: Adjust too long DESCRIPTION
+
 *beagle-4.0 (10 May 2015)
 
   10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +beagle-4.0.ebuild,

diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild
index ed32877..4686478 100644
--- a/sci-biology/beagle/beagle-4.0.ebuild
+++ b/sci-biology/beagle/beagle-4.0.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit java-pkg-2 java-ant-2
 
-DESCRIPTION="Genotype calling, genotype phasing, imputation of ungenotyped markers, identity-by-descent segment detection"
+DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers, identity-by-descent segment detection"
 HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html"
 SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip
 	http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf