[med-svn] r4245 - in trunk/packages: . beast-mcmc beast-mcmc/trunk beast-mcmc/trunk/debian

Fri Oct 23 17:37:34 UTC 2009

Author: fxf-guest
Date: 2009-10-23 17:37:34 +0000 (Fri, 23 Oct 2009)
New Revision: 4245

Added:
   trunk/packages/beast-mcmc/
   trunk/packages/beast-mcmc/tags/
   trunk/packages/beast-mcmc/trunk/
   trunk/packages/beast-mcmc/trunk/debian/
   trunk/packages/beast-mcmc/trunk/debian/changelog
   trunk/packages/beast-mcmc/trunk/debian/control
   trunk/packages/beast-mcmc/trunk/debian/copyright
   trunk/packages/beast-mcmc/trunk/debian/patches/
   trunk/packages/beast-mcmc/trunk/debian/rules
Log:
 * Iniial release of beast-mcmc



Added: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================

--- trunk/packages/beast-mcmc/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog	2009-10-23 17:37:34 UTC (rev 4245)
@@ -0,0 +1,6 @@
+beast-mcmc (1.5.2+svnr2377-1) UNRELEASED; urgency=low
+
+  * Initial release. (Closes: #552101)
+  * New upstream SVN snapshot
+
+ -- Felix Feyertag <fx at atalanta>  Fri, 23 Oct 2009 15:41:31 +0200

Added: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/control	2009-10-23 17:37:34 UTC (rev 4245)
@@ -0,0 +1,30 @@
+Source: beast-mcmc
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Felix Feyertag <felix.feyertag at googlemail.com>
+Build-Depends: debhelper (>= 7)
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/
+XS-Autobuild: yes
+Homepage: http://beast.bio.ed.ac.uk/
+
+Package: beast-mcmc
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description:  Bayesian MCMC phylogenetic inference
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular 
+ sequences. It is entirely orientated towards rooted, time-measured 
+ phylogenies inferred using strict or relaxed molecular clock models. It
+ can be used as a method of reconstructing phylogenies but is also a 
+ framework for testing evolutionary hypotheses without conditioning on a 
+ single tree topology. BEAST uses MCMC to average over tree space, so that 
+ each tree is weighted proportional to its posterior probability. Included 
+ is a simple to use user-interface program for setting up standard 
+ analyses and a suit of programs for analysing the results.
+ .
+ When publishing results using this software please cite:
+ Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by
+ sampling trees." BMC Evolutionary Biology 7:214

Added: trunk/packages/beast-mcmc/trunk/debian/copyright
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/copyright	2009-10-23 17:37:34 UTC (rev 4245)
@@ -0,0 +1,47 @@
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name: BEAST-MCMC
+Source: http://beast-mcmc.googlecode.com/svn/trunk/
+
+Copyright: 2002-2006 Alexei Drummond and Andrew Rambaut
+License: LGPL-3+
+	
+	This program is free software: you can redistribute it and/or modify
+	it under the terms of the GNU Lesser General Public License as published by
+	the Free Software Foundation, either version 3 of the License, or
+	(at your option) any later version.
+	 
+	This program 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 Lesser General Public License
+	along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
+in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
+version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
+
+License: other
+
+    BEAST includes software libraries from projects whose licensing
+    terms require that the following notices be included when they are
+    distributed in binary form and that the recipient be given a copy of
+    their respective licenses.
+    
+    This product includes software developed by the
+    JDOM Project (http://www.jdom.org/)
+    
+    This product includes software developed by
+    The Apache Software Foundation (http://www.apache.org/)
+    
+    The license for JDOM can be read in the LICENSE.txt file in the
+    source distribution available at http://www.jdom.org/
+    
+    The license for the Commons Math library can be read at
+    http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file
+    in the source distribution available at
+    http://jakarta.apache.org/commons/math/
+
+This package was debianized by Felix Feyertag <felix.feyertag at googlemail.com>.

Added: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/rules	2009-10-23 17:37:34 UTC (rev 4245)
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+PACKAGE = beast-mcmc
+SRC_VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+SVN_REVISION := $(shell echo $(SRC_VERSION) | awk -F"+" '{ print $$2 }' | sed 's/svn//' )
+TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.gz
+.PHONY: get-orig-source
+get-orig-source:
+	rm -rf get-orig-source $(TARBALL)
+	mkdir get-orig-source
+	svn export -r $(SVN_REVISION) http://beast-mcmc.googlecode.com/svn/trunk/ \
+	get-orig-source/$(PACKAGE)-$(SRC_VERSION).orig
+	GZIP=--best tar czf $(TARBALL) -C get-orig-source $(PACKAGE)-$(SRC_VERSION).orig
+	rm -rf get-orig-source
+	echo "  "$(TARBALL)" created; move it to the right destination to build the package"


Property changes on: trunk/packages/beast-mcmc/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *


