[med-svn] r6013 - in trunk/packages: . prottest prottest/trunk prottest/trunk/debian prottest/trunk/debian/source

[Andreas Tille]

Author: tille
Date: 2011-02-17 15:11:10 +0000 (Thu, 17 Feb 2011)
New Revision: 6013

Added:
   trunk/packages/prottest/
   trunk/packages/prottest/trunk/
   trunk/packages/prottest/trunk/debian/
   trunk/packages/prottest/trunk/debian/changelog
   trunk/packages/prottest/trunk/debian/compat
   trunk/packages/prottest/trunk/debian/control
   trunk/packages/prottest/trunk/debian/copyright
   trunk/packages/prottest/trunk/debian/docs
   trunk/packages/prottest/trunk/debian/rules
   trunk/packages/prottest/trunk/debian/source/
   trunk/packages/prottest/trunk/debian/source/format
   trunk/packages/prottest/trunk/debian/watch
Log:
Inject some packaging code for prottest - does not build a working package!


Added: trunk/packages/prottest/trunk/debian/changelog
===================================================================
--- trunk/packages/prottest/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/changelog	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1,5 @@
+prottest (3.0b-20101222-1) unstable; urgency=low
+
+  * Initial release (Closes: #?????)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 02 Feb 2011 15:45:54 +0100

Added: trunk/packages/prottest/trunk/debian/compat
===================================================================
--- trunk/packages/prottest/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/compat	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1 @@
+7

Added: trunk/packages/prottest/trunk/debian/control
===================================================================
--- trunk/packages/prottest/trunk/debian/control	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/control	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1,29 @@
+Source: prottest
+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 (>= 7.1)
+Standards-Version: 3.9.1
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/prottest/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/prottest/trunk/
+Homepage: http://darwin.uvigo.es/software/prottest.html
+
+Package: prottest
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Selection of best-fit models of protein evolution
+ PROTTEST (ModelTest's relative) is a program for selecting the model of
+ protein evolution that best fits a given set of sequences (alignment).
+ This java program is based on the Phyml program (for maximum likelihood
+ calculations and optimization of parameters) and uses the PAL library as
+ well. Models included are empirical substitution matrices (such as WAG,
+ LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
+ MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
+ replacement, and specific improvements (+I:invariable sites, +G: rate
+ heterogeneity among sites, +F: observed amino acid frequencies) to
+ account for the evolutionary constraints impossed by conservation of
+ protein structure and function. ProtTest uses the Akaike Information
+ Criterion (AIC) and other statistics (AICc and BIC) to find which of the
+ candidate models best fits the data at hand.

Added: trunk/packages/prottest/trunk/debian/copyright
===================================================================
--- trunk/packages/prottest/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/copyright	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1,16 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Prottest
+Upstream-Contact: David Posada <dposada at uvigo.es>
+Source: http://cs.njit.edu/usman/probalign/
+
+Files: *
+Copyright: © 2008-2011 David Posada <dposada at uvigo.es>
+License: GPL
+
+++ -> siehe THIRDPARTYLICENSES file
+
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: The Debian packaging is licensed under the same terms
+ as probalign.

Added: trunk/packages/prottest/trunk/debian/docs
===================================================================
--- trunk/packages/prottest/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/docs	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1 @@
+README

Added: trunk/packages/prottest/trunk/debian/rules
===================================================================
--- trunk/packages/prottest/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/rules	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1,10 @@
+#!/usr/bin/make -f
+# debian/rules for prottest
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@


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

Added: trunk/packages/prottest/trunk/debian/source/format
===================================================================
--- trunk/packages/prottest/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/source/format	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/prottest/trunk/debian/watch
===================================================================
--- trunk/packages/prottest/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/prottest/trunk/debian/watch	2011-02-17 15:11:10 UTC (rev 6013)
@@ -0,0 +1,2 @@
+version=3
+https://bitbucket.org/diegodl/prottest3/downloads/prottest-(.+)\.tar\.gz