[gentoo-commits] proj/sci:jlec/scilab commit in: sci-biology/pilon-bin/

[gentoo-commits] proj/sci:jlec/scilab commit in: sci-biology/pilon-bin/

[Justin Lecher]

commit:     e4f568402bfead6e32904c59ce41578b7617b851
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:35:57 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 20 21:35:57 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4f56840

sci-biology/pilon-bin: new, albeit binary package

The sources are in scala language, btw.

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/pilon-bin/metadata.xml          | 12 ++++++++++++
 sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 30 +++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/pilon-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
new file mode 100644
index 000000000..2284e6418
--- /dev/null
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-2
+
+DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
+HOMEPAGE="https://github.com/broadinstitute/pilon
+	https://github.com/broadinstitute/pilon/wiki"
+SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-java/sbt
+	>=virtual/jdk-1.5:*"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.5:*
+	>=dev-java/htsjdk-1.130"
+
+S="${WORKDIR}"
+
+src_install(){
+	cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
+	java-pkg_dojar pilon-${PV}.jar
+}

[gentoo-commits] proj/sci:jlec/scilab commit in: sci-biology/pilon-bin/

[Justin Lecher]

commit:     532f43c453327e607778d2cefaf43d45e3d04de5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 21 21:46:18 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 21 21:46:18 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=532f43c4

sci-biology/pilon-bin: Drop the scala dependency for binary build

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
index 60019723b..feeafa365 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -16,8 +16,7 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="dev-java/sbt
-	>=virtual/jdk-1.7:*"
+DEPEND=">=virtual/jdk-1.7:*"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.7:*
 	>=dev-java/htsjdk-1.130"

[gentoo-commits] proj/sci:jlec/scilab commit in: sci-biology/pilon-bin/

[Justin Lecher]

commit:     4f5a54734cb153fda873729addfb793bb1e0e6f6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 21 20:47:11 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 21 20:47:11 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f5a5473

sci-biology/pilon-bin: Fix java runtime version

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
index 2284e6418..60019723b 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -17,9 +17,9 @@ KEYWORDS="~amd64"
 IUSE=""
 
 DEPEND="dev-java/sbt
-	>=virtual/jdk-1.5:*"
+	>=virtual/jdk-1.7:*"
 RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*
+	>=virtual/jre-1.7:*
 	>=dev-java/htsjdk-1.130"
 
 S="${WORKDIR}"