[med-svn] r16814 - in trunk/packages/python-cogent/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-04-25 22:17:49 +0000 (Fri, 25 Apr 2014)
New Revision: 16814

Modified:
   trunk/packages/python-cogent/trunk/debian/README.Debian
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch
   trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch
Log:
Keep on working with the unit test


Modified: trunk/packages/python-cogent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.Debian	2014-04-25 20:28:13 UTC (rev 16813)
+++ trunk/packages/python-cogent/trunk/debian/README.Debian	2014-04-25 22:17:49 UTC (rev 16814)
@@ -22,3 +22,16 @@
 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.
 
+foldalign:  http://foldalign.ku.dk/software/
+
+guppy:      https://staff.aist.go.jp/yutaka.ueno/guppy/
+
+ilm:        ???
+
+knetfold:   http://knetfold.abcc.ncifcrf.gov/
+
+mfold:      http://mfold.rna.albany.edu/?q=mfold/download-mfold
+
+msms:       ???
+
+pplacer:    http://www.mybiosoftware.com/phylogenetic-analysis/5069

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2014-04-25 20:28:13 UTC (rev 16813)
+++ trunk/packages/python-cogent/trunk/debian/control	2014-04-25 22:17:49 UTC (rev 16814)
@@ -18,6 +18,9 @@
                clustalw,
                dialign,
                infernal,
+               mafft,
+               mothur,
+               muscle,
                parsinsert
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-cogent/trunk/

Modified: trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch	2014-04-25 20:28:13 UTC (rev 16813)
+++ trunk/packages/python-cogent/trunk/debian/patches/fasttree_not_in_caps.patch	2014-04-25 22:17:49 UTC (rev 16814)
@@ -3,9 +3,9 @@
 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 @@
+--- a/cogent/app/fasttree.py
++++ b/cogent/app/fasttree.py
+@@ -25,7 +25,7 @@ __status__ = "Development"
  class FastTree(CommandLineApplication):
      """FastTree application Controller"""
  
@@ -14,3 +14,14 @@
      _input_handler = '_input_as_multiline_string'
      _parameters = {
              '-quiet':FlagParameter('-',Name='quiet'),
+--- a/cogent/app/fasttree_v1.py
++++ b/cogent/app/fasttree_v1.py
+@@ -20,7 +20,7 @@ __status__ = "Development"
+ 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/parsinsert_not_in_caps.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	2014-04-25 20:28:13 UTC (rev 16813)
+++ trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	2014-04-25 22:17:49 UTC (rev 16814)
@@ -3,9 +3,9 @@
 Description: make script compatible with spelling of Debian's
  parsinsert package
 
---- PyCogent-1.5.3.orig/cogent/app/parsinsert.py
-+++ PyCogent-1.5.3/cogent/app/parsinsert.py
-@@ -28,7 +28,7 @@
+--- a/cogent/app/parsinsert.py
++++ b/cogent/app/parsinsert.py
+@@ -28,7 +28,7 @@ from StringIO import StringIO
  class ParsInsert(CommandLineApplication):
      """ParsInsert application Controller"""
  
@@ -14,3 +14,34 @@
      _input_handler = '_input_as_multiline_string'
      _parameters = {
                      # read mask from this file
+--- a/tests/test_app/test_parsinsert.py
++++ b/tests/test_app/test_parsinsert.py
+@@ -60,7 +60,7 @@ class ParsInsertTests(TestCase):
+         
+         app = ParsInsert()
+         self.assertEqual(app.BaseCommand, \
+-                         ''.join(['cd "',getcwd(),'/"; ','ParsInsert']))
++                         ''.join(['cd "',getcwd(),'/"; ','parsinsert']))
+         
+     def test_change_working_dir(self):
+         """Change working dir"""
+@@ -68,7 +68,7 @@ class ParsInsertTests(TestCase):
+         app = ParsInsert(WorkingDir='/tmp/ParsInsertTest')
+         self.assertEqual(app.BaseCommand, \
+                        ''.join(['cd "','/tmp/ParsInsertTest',\
+-                                '/"; ','ParsInsert']))
++                                '/"; ','parsinsert']))
+                                 
+         rmtree('/tmp/ParsInsertTest')
+ 
+--- a/tests/alltests.py
++++ b/tests/alltests.py
+@@ -229,7 +229,7 @@ def suite():
+             ('mothur', 'test_mothur'),
+             ('muscle', 'test_muscle_v38'),
+             ('msms', 'test_msms'),
+-            ('ParsInsert', 'test_parsinsert'),
++            ('parsinsert', 'test_parsinsert'),
+             ('pplacer', 'test_pplacer'),
+             ('rdp_classifier-2.2.jar', 'test_rdp_classifier'),
+             ('rdp_classifier-2.0.jar', 'test_rdp_classifier20'),