details: http://www.bx.psu.edu/hg/galaxy/rev/dac542cca894 changeset: 2937:dac542cca894 user: Nate Coraor nate@bx.psu.edu date: Fri Oct 30 14:27:48 2009 -0400 description: Fix a bug in file staging
diffstat:
lib/galaxy/jobs/runners/pbs.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-)
diffs (12 lines):
diff -r 583fab0515a0 -r dac542cca894 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Fri Oct 30 12:51:07 2009 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Fri Oct 30 14:27:48 2009 -0400 @@ -217,7 +217,7 @@
# write the job script if self.app.config.pbs_stage_path != '': - script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) + script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_files), self.app.config.pbs_stage_path, exec_dir, command_line) else: if self.app.config.set_metadata_externally: external_metadata_script = job_wrapper.setup_external_metadata( exec_dir = exec_dir, tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, output_fnames = output_fnames, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior