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

[Martin Mokrejs]

commit:     078f19efedf1e0abfa70e43de79bb284aa6578dc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 21:42:40 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 21:42:40 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=078f19ef

sci-biology/cgview-bin: new package, needs java team testing, maybe dev-java/batik is misisng svg USE flag?

Package-Manager: portage-2.2.7

---
 sci-biology/cgview-bin/ChangeLog                  | 10 ++++++
 sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 44 +++++++++++++++++++++++
 sci-biology/cgview-bin/metadata.xml               |  9 +++++
 3 files changed, 63 insertions(+)

diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog
new file mode 100644
index 0000000..d8d6b14
--- /dev/null
+++ b/sci-biology/cgview-bin/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/cgview-bin
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cgview-bin-20131130 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +cgview-bin-20131130.ebuild, +metadata.xml:
+  sci-biology/cgview-bin: new package, needs java team testing, maybe dev-
+  java/batik is misisng svg USE flag?

diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
new file mode 100644
index 0000000..be563a9
--- /dev/null
+++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+# download 134MB in size!
+DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
+HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
+SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=dev-lang/perl-5.8.8
+		>=sci-biology/ncbi-tools-2.2.15
+		>=virtual/jre-1.4.2
+		dev-java/xerces
+		dev-java/batik
+		dev-java/commons-lang
+		>=media-gfx/imagemagick-6
+		>=sci-biology/bioperl-1.4.0"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/cgview_comparison_tool
+
+src_install() {
+	echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview"
+	echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
+	doenvd "${S}/99cgview" || die
+	#export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin
+	#export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"
+
+	dobin bin/cgview.jar
+}
+
+src_test(){
+	./update_cogs.sh || die
+	./test.sh || die
+}

diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cgview-bin/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@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>