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

["Justin Lecher" <jlec@gentoo.org>]

commit:     420e46ff1a1f7709757fae778140fb53c24189d0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 19:02:45 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 19:02:45 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=420e46ff

sci-biology/artemis: Switch from git-2 to git-r3

Package-Manager: portage-2.2.8

---
 sci-biology/artemis/ChangeLog           |  6 +++++-
 sci-biology/artemis/artemis-9999.ebuild | 34 ++++++++++-----------------------
 sci-biology/artemis/metadata.xml        | 10 +++++-----
 3 files changed, 20 insertions(+), 30 deletions(-)

diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index a992d60..56cbedc 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/artemis
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild,
+  metadata.xml:
+  Switch from git-2 to git-r3
+
   07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
   sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
 

diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 4481975..ca3ddf1 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -1,23 +1,15 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-2
+inherit java-pkg-2 java-ant-2 git-r3
 
 DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
-	KEYWORDS="~amd64 ~x86"
-else
-	SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -25,19 +17,13 @@ KEYWORDS=""
 IUSE=""
 
 # uses its own BamView
-DEPEND="sci-biology/samtools
-		>=virtual/jdk-1.5
-		>=dev-java/sun-jdk-1.5
-		dev-java/ant-core"
+DEPEND="
+	sci-biology/samtools
+	>=virtual/jdk-1.5
+	dev-java/ant-core"
 RDEPEND="${DEPEND}
-		>=virtual/jre-1.5"
+	>=virtual/jre-1.5"
 
 # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
 # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
 # http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
-src_compile() {
-	emake || die
-	# 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
index 07b5255..2bc8930 100644
--- a/sci-biology/artemis/metadata.xml
+++ b/sci-biology/artemis/metadata.xml
@@ -1,9 +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>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>