[med-svn] r16437 - in trunk/packages/python-biopython/trunk/debian: . patches

[Philipp Benner]

Author: philipp
Date: 2014-03-12 18:09:16 +0000 (Wed, 12 Mar 2014)
New Revision: 16437

Added:
   trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
Modified:
   trunk/packages/python-biopython/trunk/debian/changelog
   trunk/packages/python-biopython/trunk/debian/patches/series
   trunk/packages/python-biopython/trunk/debian/rules
Log:
DSSP fix; excluded BioSQL_MySQLdb BioSQL_psycopg2 which require internet access


Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog	2014-03-12 13:14:56 UTC (rev 16436)
+++ trunk/packages/python-biopython/trunk/debian/changelog	2014-03-12 18:09:16 UTC (rev 16437)
@@ -35,7 +35,7 @@
   * Standards version 3.9.4
 
  -- Philipp Benner <philipp at debian.org>  Thu, 14 Feb 2013 22:08:04 +0100
-  
+
 python-biopython (1.60-1) unstable; urgency=low
 
   * New upstream release.

Added: trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch	2014-03-12 18:09:16 UTC (rev 16437)
@@ -0,0 +1,39 @@
+Index: python-biopython-1.63/Bio/PDB/DSSP.py
+===================================================================
+--- python-biopython-1.63.orig/Bio/PDB/DSSP.py	2014-03-12 17:58:51.000000000 +0000
++++ python-biopython-1.63/Bio/PDB/DSSP.py	2014-03-12 18:00:02.000000000 +0000
+@@ -80,7 +80,7 @@
+     assert 0
+ 
+ 
+-def dssp_dict_from_pdb_file(in_file, DSSP="dssp"):
++def dssp_dict_from_pdb_file(in_file, DSSP="mkdssp"):
+     """
+     Create a DSSP dictionary from a PDB file.
+ 
+@@ -199,7 +199,7 @@
+         -42.399999999999999)
+     """
+ 
+-    def __init__(self, model, pdb_file, dssp="dssp"):
++    def __init__(self, model, pdb_file, dssp="mkdssp"):
+         """
+         @param model: the first model of the structure
+         @type model: L{Model}
+Index: python-biopython-1.63/Tests/test_DSSP_tool.py
+===================================================================
+--- python-biopython-1.63.orig/Tests/test_DSSP_tool.py	2014-03-12 17:59:10.000000000 +0000
++++ python-biopython-1.63/Tests/test_DSSP_tool.py	2014-03-12 17:59:33.000000000 +0000
+@@ -22,10 +22,10 @@
+ try:
+     try:
+         # Newer versions of DSSP
+-        subprocess.check_call(["dssp", "--version"], **quiet_kwargs)
++        subprocess.check_call(["mkdssp", "--version"], **quiet_kwargs)
+     except subprocess.CalledProcessError:
+         # Older versions of DSSP
+-        subprocess.check_call(["dssp", "-h"], **quiet_kwargs)
++        subprocess.check_call(["mkdssp", "-h"], **quiet_kwargs)
+ except OSError:
+     raise MissingExternalDependencyError(
+         "Install dssp if you want to use it from Biopython.")

Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	2014-03-12 13:14:56 UTC (rev 16436)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2014-03-12 18:09:16 UTC (rev 16437)
@@ -1 +1,2 @@
 fix_test_emboss.patch
+fix_dssp.patch

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-03-12 13:14:56 UTC (rev 16436)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-03-12 18:09:16 UTC (rev 16437)
@@ -32,7 +32,7 @@
 	mkdir -p Tests_avoid
 	for avoid in \
 			Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS \
-			PAML_tools EmbossPhylipNew \
+			PAML_tools EmbossPhylipNew BioSQL_MySQLdb BioSQL_psycopg2 \
 			MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
 			$(EXCLUDEBWA) \
 		    ; do \