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

[Martin Mokrejs]

commit:     116a34b4a030050965fddb6fda334062ef424105
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:09:18 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:09:18 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=116a34b4

sci-biology/artemis-bin: version bump, added a link to INSTALL docs

Package-Manager: portage-2.2.7

---
 sci-biology/artemis-bin/ChangeLog                        |  9 +++++++--
 ...emis-bin-13.2.12.ebuild => artemis-bin-16.0.6.ebuild} | 16 +++++++++++++---
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index 9885717..6cd5bd4 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/artemis-bin
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*artemis-bin-16.0.6 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +artemis-bin-16.0.6.ebuild, -artemis-bin-13.2.12.ebuild:
+  sci-biology/artemis-bin: version bump, added a link to INSTALL docs
+
   03 Mar 2013; Justin Lecher <jlec@g.o> artemis-bin-13.2.12.ebuild,
   metadata.xml:
   Clean whitespace errors
@@ -11,4 +17,3 @@
   08 Jan 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
   +artemis-bin-13.2.12.ebuild, +metadata.xml:
   initial, not yet working ebuild
-

diff --git a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
similarity index 51%
rename from sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
rename to sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
index fa1edc3..528d3e8 100644
--- a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
@@ -6,9 +6,12 @@ EAPI=3
 
 inherit java-pkg-2
 
+MY_V="16"
+
 DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
+	ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -16,6 +19,13 @@ KEYWORDS=""
 IUSE=""
 
 DEPEND="sci-biology/samtools
-		sci-biology/bamview"
+		sci-biology/bambino" # aka BamView
 RDEPEND="${DEPEND}
-		>=virtual/jre-1.5"
+		>=virtual/jre-1.6"
+
+src_install(){
+	dodoc artemis.pdf
+}
+
+# do not know what is the diffeerence between artemis_compiled_v16.0.6.tar.gz, artemis_v16.0.6.jar and sartemis_v16.0.6.jar
+#   ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.6/