[med-svn] r16794 - in trunk/packages/python-cogent/trunk/debian: . patches

[Timothy Booth]

Author: tbooth-guest
Date: 2014-04-25 16:29:31 +0000 (Fri, 25 Apr 2014)
New Revision: 16794

Added:
   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/changelog
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/patches/series
Log:
Patches to get cogent working with newer cd-hit and parsinsert


Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2014-04-25 16:02:13 UTC (rev 16793)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2014-04-25 16:29:31 UTC (rev 16794)
@@ -1,3 +1,14 @@
+python-cogent (1.5.3-2biolinux1) trusty; urgency=low
+
+  * Allow use of newer cd-hit that doesn't leave a tmp file
+    Note - the tests still fail as output is different, but
+    this is a quick fix.
+  * Also make the script compatible with our parsinsert package
+  * Add suggests dep on both of these
+  * Rebuild for Trusty
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 25 Apr 2014 17:27:42 +0100
+
 python-cogent (1.5.3-2) unstable; urgency=low
 
   * debian/rules: Add -f option to rm statements to not fail if

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2014-04-25 16:02:13 UTC (rev 16793)
+++ trunk/packages/python-cogent/trunk/debian/control	2014-04-25 16:29:31 UTC (rev 16794)
@@ -15,7 +15,7 @@
 Package: python-cogent
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
-Suggests: python-cogent-doc
+Suggests: python-cogent-doc, cd-hit, parsinsert
 Description: framework for genomic biology
  PyCogent is a software library for genomic biology. It is a fully
  integrated and thoroughly tested framework for:

Added: trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit	2014-04-25 16:29:31 UTC (rev 16794)
@@ -0,0 +1,29 @@
+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)
+ 

Added: trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps	2014-04-25 16:29:31 UTC (rev 16794)
@@ -0,0 +1,11 @@
+--- 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 16:02:13 UTC (rev 16793)
+++ trunk/packages/python-cogent/trunk/debian/patches/series	2014-04-25 16:29:31 UTC (rev 16794)
@@ -1 +1,2 @@
+accept_newer_cdhit
 fix_python_shebang_line.patch