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 <[email protected]> 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 \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
