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

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

commit:     1afb461b204933db48bfe976a37203c92846930d
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan  8 15:49:57 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan  8 15:49:57 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1afb461b

sci-biology/artemis: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool

---
 sci-biology/artemis/ChangeLog           |   10 ++++++++
 sci-biology/artemis/artemis-9999.ebuild |   39 +++++++++++++++++++++++++++++++
 sci-biology/artemis/metadata.xml        |    9 +++++++
 3 files changed, 58 insertions(+), 0 deletions(-)

diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
new file mode 100644
index 0000000..8a33496
--- /dev/null
+++ b/sci-biology/artemis/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/artemis
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*artemis-9999 (08 Jan 2012)
+
+  08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +artemis-9999.ebuild, +metadata.xml:
+  initial, not yet working ebuild
+

diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
new file mode 100644
index 0000000..ff8d52d
--- /dev/null
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
+
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
+	KEYWORDS=""
+else
+	SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sci-biology/samtools
+		sci-biology/bamview
+		>=virtual/jdk-1.5
+		>=dev-java/sun-jdk-1.5
+		dev-java/ant-core"
+RDEPEND="${DEPEND}
+		>=virtual/jre-1.5"
+
+src_compile() {
+	ant compile || die
+
+	einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline"
+}

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