[med-svn] r16808 - trunk/packages/python-cogent/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-04-25 19:19:18 +0000 (Fri, 25 Apr 2014)
New Revision: 16808

Added:
   trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch
   trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch
Removed:
   trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit
   trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps
Modified:
   trunk/packages/python-cogent/trunk/debian/patches/series
Log:
DEP3


Deleted: trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit	2014-04-25 19:15:05 UTC (rev 16807)
+++ trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit	2014-04-25 19:19:18 UTC (rev 16808)
@@ -1,29 +0,0 @@
-Get Cogent to work with newer CD-HIT that doesn't leave
-a temporary file sitting around.  This patch has only been quickly tested and
-there may be deeper issues.
---- a/cogent/app/cd_hit.py
-+++ b/cogent/app/cd_hit.py
-@@ -257,7 +257,10 @@
-     # perform cleanup
-     res.cleanUp()
-     shutil.rmtree(working_dir)
--    remove(params['-o'] + '.bak.clstr')
-+    try:
-+	remove(params['-o'] + '.bak.clstr')
-+    except OSError:
-+	pass #maybe there was no file
- 
-     return remapped_clusters
- 
-@@ -299,7 +302,10 @@
-     # perform cleanup
-     res.cleanUp()
-     shutil.rmtree(working_dir)
--    remove(params['-o'] + '.bak.clstr')
-+    try:
-+	remove(params['-o'] + '.bak.clstr')
-+    except OSError:
-+	pass #maybe there was no file
- 
-     return SequenceCollection(new_seqs, MolType=moltype)
- 

Copied: trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch (from rev 16795, trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit)
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch	2014-04-25 19:19:18 UTC (rev 16808)
@@ -0,0 +1,32 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Changed: Fri, 25 Apr 2014 17:27:42 +0100
+Description: Get Cogent to work with newer CD-HIT that doesn't leave
+ a temporary file sitting around.  This patch has only been quickly tested and
+ there may be deeper issues.
+
+--- a/cogent/app/cd_hit.py
++++ b/cogent/app/cd_hit.py
+@@ -257,7 +257,10 @@
+     # perform cleanup
+     res.cleanUp()
+     shutil.rmtree(working_dir)
+-    remove(params['-o'] + '.bak.clstr')
++    try:
++	remove(params['-o'] + '.bak.clstr')
++    except OSError:
++	pass #maybe there was no file
+ 
+     return remapped_clusters
+ 
+@@ -299,7 +302,10 @@
+     # perform cleanup
+     res.cleanUp()
+     shutil.rmtree(working_dir)
+-    remove(params['-o'] + '.bak.clstr')
++    try:
++	remove(params['-o'] + '.bak.clstr')
++    except OSError:
++	pass #maybe there was no file
+ 
+     return SequenceCollection(new_seqs, MolType=moltype)
+ 

Deleted: trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps	2014-04-25 19:15:05 UTC (rev 16807)
+++ trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps	2014-04-25 19:19:18 UTC (rev 16808)
@@ -1,11 +0,0 @@
---- a/cogent/app/parsinsert.py
-+++ b/cogent/app/parsinsert.py
-@@ -28,7 +28,7 @@
- class ParsInsert(CommandLineApplication):
-     """ParsInsert application Controller"""
- 
--    _command = 'ParsInsert'
-+    _command = 'parsinsert'
-     _input_handler = '_input_as_multiline_string'
-     _parameters = {
-                     # read mask from this file

Copied: trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch (from rev 16795, trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps)
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	2014-04-25 19:19:18 UTC (rev 16808)
@@ -0,0 +1,16 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Fri, 25 Apr 2014 17:27:42 +0100
+Description: make script compatible with spelling of Debian's
+ parsinsert package
+
+--- a/cogent/app/parsinsert.py
++++ b/cogent/app/parsinsert.py
+@@ -28,7 +28,7 @@
+ class ParsInsert(CommandLineApplication):
+     """ParsInsert application Controller"""
+ 
+-    _command = 'ParsInsert'
++    _command = 'parsinsert'
+     _input_handler = '_input_as_multiline_string'
+     _parameters = {
+                     # read mask from this file

Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series	2014-04-25 19:15:05 UTC (rev 16807)
+++ trunk/packages/python-cogent/trunk/debian/patches/series	2014-04-25 19:19:18 UTC (rev 16808)
@@ -1,2 +1,3 @@
-accept_newer_cdhit
+accept_newer_cdhit.patch
 fix_python_shebang_line.patch
+parsinsert_not_in_caps.patch