fixes

broadinstitute · Apr 17, 2015 · f5b0a70 · f5b0a70
1 parent b308cfb
commit f5b0a70
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/tools/mosaik.py b/tools/mosaik.py
@@ -2,8 +2,8 @@
     The MOSAIK aligner
 '''
 
-import logging, tools
-import os, os.path, subprocess
+import logging, os, os.path, subprocess
+import tools, util.file
 
 tool_version = '2.1.33'
 url = 'https://mosaik-aligner.googlecode.com/files/MOSAIK-{ver}-{os}.tar'

diff --git a/tools/novoalign.py b/tools/novoalign.py
@@ -175,7 +175,7 @@ def index_fasta(self, refFasta):
         try:
             mode = os.stat(outfname).st_mode & ~stat.S_IXUSR & ~stat.S_IXGRP & ~stat.S_IXOTH
             os.chmod(outfname, mode)
-        except (IOError, OSError) as e:
+        except (IOError, OSError):
             pass
 
 

diff --git a/tools/vphaser2.py b/tools/vphaser2.py
@@ -72,7 +72,7 @@ def _get_vphaser2_path() :
     elif uname[0] == 'Linux' and uname[4].endswith('64') :
         osName = 'linux64'
     else :
-        log.debug('V-Phaser 2 not implemented for OS %s %s'
+        log.debug('V-Phaser 2 not implemented for OS %s %s',
             uname[0], uname[4])
         return ''
     binariesPath = util.file.get_binaries_path()