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

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

commit:     aeb330b5d14397ab0a558befd4ff1434a6835e91
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:18:44 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:18:44 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aeb330b5

sci-biology/act-bin: new java package with upstream binaries

Package-Manager: portage-2.2.28

 sci-biology/act-bin/act-bin-13.0.0.ebuild | 50 +++++++++++++++++++++++++++++++
 sci-biology/act-bin/metadata.xml          | 12 ++++++++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/act-bin/act-bin-13.0.0.ebuild b/sci-biology/act-bin/act-bin-13.0.0.ebuild
new file mode 100644
index 0000000..debf770
--- /dev/null
+++ b/sci-biology/act-bin/act-bin-13.0.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-2
+
+DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/sact_v13.jar
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_v13.jar
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_html_build.zip -> ${P}.html_build.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	!sci-biology/artemis"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.6:*"
+
+S="${WORKDIR}"
+
+src_unpack(){
+	unzip "${DISTDIR}"/${P}.html_build.zip || die
+}
+
+src_prepare(){
+	default
+	cd act_html_build || die
+	rm -f .DS_Store HTML.index HTML.manifest || die
+}
+
+src_install(){
+	java-pkg_dojar "${DISTDIR}"/*.jar
+	dodoc "${DISTDIR}"/${P}.manual.pdf
+	insinto /usr/share/doc/"${PN}"/html
+	doins act_html_build/*
+}
+
+pkg_postinst(){
+	einfo "For BAM file support please install sci-biology/BamView"
+	einfo "You may find interesting the additional web resources:"
+	einfo "http://www.webact.org/WebACT"
+	einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
+}

diff --git a/sci-biology/act-bin/metadata.xml b/sci-biology/act-bin/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/act-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>