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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     a7bf4e9d7d31c5c27213f618b1160b0d7006ac1c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 18:15:12 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 18:15:12 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7bf4e9d

sci-biology/bambino: a new package, maybe should have -bin in its name?; needs decent inspection from java team for sure

Package-Manager: portage-2.2.7

---
 sci-biology/bambino/ChangeLog           | 11 ++++++++++
 sci-biology/bambino/bambino-1.02.ebuild | 36 +++++++++++++++++++++++++++++++++
 sci-biology/bambino/bambino-1.06.ebuild | 36 +++++++++++++++++++++++++++++++++
 sci-biology/bambino/metadata.xml        |  9 +++++++++
 4 files changed, 92 insertions(+)

diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog
new file mode 100644
index 0000000..1cc049f
--- /dev/null
+++ b/sci-biology/bambino/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/bambino
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bambino-1.02 (23 Mar 2014)
+*bambino-1.06 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bambino-1.02.ebuild, +bambino-1.06.ebuild, +metadata.xml:
+  sci-biology/bambino: a new package, maybe should have -bin in its name?; needs
+  decent inspection from java team for sure

diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
new file mode 100644
index 0000000..4ea6c9d
--- /dev/null
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 eutils
+
+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+
+# bug #377305
+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar
+		https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.02.jar"
+
+LICENSE="bambino"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	>=virtual/jdk-1.6
+	sci-biology/picard
+	dev-java/jdbc-mysql"
+
+src_install(){
+	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
+	doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
+	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+
+	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'"
+	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'"
+	einfo "More info at "${HOMEPAGE}
+
+}

diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
new file mode 100644
index 0000000..864beee
--- /dev/null
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 eutils
+
+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+
+# bug #377305
+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar
+		https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.06.jar"
+
+LICENSE="bambino"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	>=virtual/jdk-1.6
+	sci-biology/picard
+	dev-java/jdbc-mysql"
+
+src_install(){
+	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
+	doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
+	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+
+	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'"
+	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'"
+	einfo "More info at "${HOMEPAGE}
+
+}

diff --git a/sci-biology/bambino/metadata.xml b/sci-biology/bambino/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/bambino/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>