details: http://www.bx.psu.edu/hg/galaxy/rev/ecbd01636a92 changeset: 3761:ecbd01636a92 user: Nate Coraor <nate@bx.psu.edu> date: Mon May 10 11:22:50 2010 -0400 description: Bug in SGE external metadata diffstat: lib/galaxy/jobs/runners/sge.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (17 lines): diff -r f53d06cf2f93 -r ecbd01636a92 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:22:50 2010 -0400 @@ -166,12 +166,11 @@ script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) if self.app.config.set_metadata_externally: - output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] script += "cd %s\n" % os.path.abspath( os.getcwd() ) script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = output_fnames, + output_fnames = job_wrapper.get_output_fnames(), set_extension = False, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" )