[med-svn] r9676 - in trunk/packages: . phyutility phyutility/trunk phyutility/trunk/debian phyutility/trunk/debian/source

[Andreas Tille]

Author: tille
Date: 2012-02-16 07:35:03 +0000 (Thu, 16 Feb 2012)
New Revision: 9676

Added:
   trunk/packages/phyutility/
   trunk/packages/phyutility/trunk/
   trunk/packages/phyutility/trunk/debian/
   trunk/packages/phyutility/trunk/debian/changelog
   trunk/packages/phyutility/trunk/debian/compat
   trunk/packages/phyutility/trunk/debian/control
   trunk/packages/phyutility/trunk/debian/copyright
   trunk/packages/phyutility/trunk/debian/rules
   trunk/packages/phyutility/trunk/debian/source/
   trunk/packages/phyutility/trunk/debian/source/format
   trunk/packages/phyutility/trunk/debian/watch
Log:
Inject some preliminary packaging stuff for phyutility; UNTESTED!  will need some time to finish, volunteers welcome


Added: trunk/packages/phyutility/trunk/debian/changelog
===================================================================
--- trunk/packages/phyutility/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/changelog	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1,5 @@
+phyutility (2.2.4-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #?????)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 21 Feb 2011 08:17:38 +0100

Added: trunk/packages/phyutility/trunk/debian/compat
===================================================================
--- trunk/packages/phyutility/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/compat	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1 @@
+8

Added: trunk/packages/phyutility/trunk/debian/control
===================================================================
--- trunk/packages/phyutility/trunk/debian/control	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/control	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1,37 @@
+Source: phyutility
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 8), javahelper (>=0.25), openjdk-6-jdk, ant, libjebl2-java,
+Standards-Version: 3.9.2
+Homepage: http://code.google.com/p/phyutility/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phyutility/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phyutility/trunk/
+
+Package: phyutility
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}
+Description: simple analyses or modifications on both phylogenetic trees and data matrices
+ Phyutility (fyoo-til-i-te) is a command line program that performs
+ simple analyses or modifications on both trees and data matrices.
+ .
+ Currently it performs the following functions (to suggest another
+ feature, submit an Issue and use the label Type-Enhancement) :
+ .
+ Trees
+  * rerooting
+  * pruning
+  * type conversion
+  * consensus
+  * leaf stability
+  * lineage movement
+  * tree support 
+ .
+ Data Matrices
+  * concatenate alignments
+  * genbank parsing
+  * trimming alignments
+  * search NCBI
+  * fetch NCBI

Added: trunk/packages/phyutility/trunk/debian/copyright
===================================================================
--- trunk/packages/phyutility/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/copyright	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1,30 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: phyutility
+Upstream-Contact: Stephen Smith <blackrim at gmail.com>
+Source: http://code.google.com/p/phyutility/downloads
+
+Files: *
+Copyright: © 2007-2012 Stephen Smith <blackrim at gmail.com>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Andreas Tille <tille at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in
+ "/usr/share/common-licenses/GPL-3".

Added: trunk/packages/phyutility/trunk/debian/rules
===================================================================
--- trunk/packages/phyutility/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/rules	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+	dh $@ --with javahelper
+
+get-orig-source:
+	uscan --verbose --force-download


Property changes on: trunk/packages/phyutility/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/phyutility/trunk/debian/source/format
===================================================================
--- trunk/packages/phyutility/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/source/format	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/phyutility/trunk/debian/watch
===================================================================
--- trunk/packages/phyutility/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/phyutility/trunk/debian/watch	2012-02-16 07:35:03 UTC (rev 9676)
@@ -0,0 +1,3 @@
+version=3
+opts="dversionmangle=s/\./_/g" \
+   http://googlecode.debian.net/p/phyutility/phyutility_(.+)\.tar\.gz