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When using the local job runner, run tools in the generated working directory, providing absolute paths.

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This commit is contained in:
Daniel Blankenberg
2007-10-05 01:25:42 +00:00
parent 96a90a5072
commit 6777c4ef35
2 changed files with 20 additions and 3 deletions
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lib/galaxy/jobs/runners/local.py
+1
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@@ -53,6 +53,7 @@ class LocalJobRunner( object ):
log.debug( 'executing: %s' % command_line )
proc = subprocess.Popen( args = command_line,
shell = True,
cwd = job_wrapper.working_directory,
stdout = subprocess.PIPE,
stderr = subprocess.PIPE )
stdout = proc.stdout.read()
lib/galaxy/tools/__init__.py
+19 -3
View File
@@ -194,7 +194,14 @@ class Tool:
self.command = command.text.lstrip() # get rid of leading whitespace
interpreter = command.get("interpreter")
if interpreter:
self.command = interpreter + " " + os.path.join(self.tool_dir, self.command)
#if not using pbs, change command to absolute path
if not self.app.config.use_pbs:
executable = self.command.split()[0]
abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable))
self.command = self.command.replace(executable, abs_executable, 1)
self.command = interpreter + " " + self.command
else:
self.command = interpreter + " " + os.path.join(self.tool_dir, self.command)
else:
self.command = ''
# Short description of the tool
@@ -782,14 +789,23 @@ class Tool:
for name, data in output_datasets.items():
param_dict[name] = DatasetFilenameWrapper( data )
# Provide access to a path to store additional files
param_dict[name].files_path = os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) )
if self.app.config.use_pbs:
param_dict[name].files_path = os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) )
else:
param_dict[name].files_path = os.path.abspath(os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) ))
for child_association in data.children:
child = child_association.child
key = "_CHILD___%s___%s" % ( name, child.designation )
param_dict[ key ] = DatasetFilenameWrapper( child )
# We add access to app here, this allows access to app.config, etc
param_dict['__app__'] = RawObjectWrapper( self.app )
param_dict['__new_file_path__'] = self.app.config.new_file_path #More convienent access to this value; we don't need to wrap a string
# More convienent access to app.config.new_file_path; we don't need to wrap a string
# But this method of generating additional datasets should be considered DEPRECATED
if self.app.config.use_pbs:
param_dict['__new_file_path__'] = self.app.config.new_file_path
else:
param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path)
# Return the dictionary of parameters
return param_dict