[med-svn] r16813 - in trunk/packages/python-cogent/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-04-25 20:28:13 +0000 (Fri, 25 Apr 2014)
New Revision: 16813

Added:
   trunk/packages/python-cogent/trunk/debian/README.Debian
   trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch
Modified:
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/copyright
   trunk/packages/python-cogent/trunk/debian/patches/series
   trunk/packages/python-cogent/trunk/debian/rules
Log:
Start working on the test suite


Added: trunk/packages/python-cogent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/README.Debian	2014-04-25 20:28:13 UTC (rev 16813)
@@ -0,0 +1,24 @@
+PyCogent for Debian
+-------------------
+
+The following external tools are supported by PyCogent but not yet
+packaged for Debian:
+
+
+blat:       http://anonscm.debian.org/gitweb/?p=debian-med/blat.git
+            Packaging prepared but licensing issues
+
+carnac:     http://bioinfo.lifl.fr/carnac/
+
+cmfinder:   http://bio.cs.washington.edu/yzizhen/CMfinder/
+
+comrna:     http://stormo.wustl.edu/comRNA/
+
+contrafold: http://contra.stanford.edu/contrafold/
+	    http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract
+
+covea:      ???
+
+dynalign:   http://rna.urmc.rochester.edu/dynalign.html
+            Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J. Mol. Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
+

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2014-04-25 19:49:37 UTC (rev 16812)
+++ trunk/packages/python-cogent/trunk/debian/control	2014-04-25 20:28:13 UTC (rev 16813)
@@ -10,7 +10,15 @@
                python-support,
                python-numpy,
                python-sphinx,
-               cython
+               cython,
+               blast2,
+               bwa,
+               cd-hit,
+               clearcut,
+               clustalw,
+               dialign,
+               infernal,
+               parsinsert
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-cogent/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-cogent/trunk/

Modified: trunk/packages/python-cogent/trunk/debian/copyright
===================================================================
--- trunk/packages/python-cogent/trunk/debian/copyright	2014-04-25 19:49:37 UTC (rev 16812)
+++ trunk/packages/python-cogent/trunk/debian/copyright	2014-04-25 20:28:13 UTC (rev 16813)
@@ -60,5 +60,5 @@
 License: GPL-2
 
 License: GPL-2
- On Debian systems you can find the full text of the GNU Public License
- version 2 at `/usr/share/common-licenses/GPL-2'.
+ On Debian systems you can find the full text of the GNU General Public
+ License version 2 at `/usr/share/common-licenses/GPL-2'.

Added: trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch	2014-04-25 20:28:13 UTC (rev 16813)
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 25 Apr 2014 21:27:42 +0100
+Description: make script compatible with spelling of Debian's
+ fasttree package
+
+--- PyCogent-1.5.3.orig/cogent/app/fasttree.py
++++ PyCogent-1.5.3/cogent/app/fasttree.py
+@@ -25,7 +25,7 @@
+ class FastTree(CommandLineApplication):
+     """FastTree application Controller"""
+ 
+-    _command = 'FastTree'
++    _command = 'fasttree'
+     _input_handler = '_input_as_multiline_string'
+     _parameters = {
+             '-quiet':FlagParameter('-',Name='quiet'),

Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series	2014-04-25 19:49:37 UTC (rev 16812)
+++ trunk/packages/python-cogent/trunk/debian/patches/series	2014-04-25 20:28:13 UTC (rev 16813)
@@ -1,3 +1,4 @@
 accept_newer_cdhit.patch
 fix_python_shebang_line.patch
 parsinsert_not_in_caps.patch
+fasttree_not_in_caps.patch

Modified: trunk/packages/python-cogent/trunk/debian/rules
===================================================================
--- trunk/packages/python-cogent/trunk/debian/rules	2014-04-25 19:49:37 UTC (rev 16812)
+++ trunk/packages/python-cogent/trunk/debian/rules	2014-04-25 20:28:13 UTC (rev 16813)
@@ -42,6 +42,9 @@
 override_dh_strip:
 	dh_strip --dbg-package=python-cogent-dbg
 
+override_dh_auto_test:
+	$(CURDIR)/run_tests
+
 get-orig-source:
 	mkdir -p ../tarballs
 	uscan --verbose --force-download --destdir=../tarballs