details: http://www.bx.psu.edu/hg/galaxy/rev/cf17b5a16eff changeset: 1513:cf17b5a16eff user: Nate Coraor nate@bx.psu.edu date: Wed Sep 17 10:45:20 2008 -0400 description: Quick 'n easy solution to the EMBOSS stage in/out problem: read the outputs from the "real" galaxy path instead of the temp stage path.

1 file(s) affected in this change:

lib/galaxy/jobs/runners/pbs.py

diffs (31 lines):

diff -r 1e408bab8941 -r cf17b5a16eff lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Tue Sep 16 15:23:23 2008 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Sep 17 10:45:20 2008 -0400 @@ -146,7 +146,7 @@ if self.app.config.pbs_application_server: pbs_ofile = self.app.config.pbs_application_server + ':' + ofile pbs_efile = self.app.config.pbs_application_server + ':' + efile - stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames() ) + stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames(), symlink=True ) stageout = self.get_stage_in_out( job_wrapper.get_output_fnames() ) job_attrs = pbs.new_attropl(5) job_attrs[0].name = pbs.ATTR_o @@ -372,15 +372,15 @@ self.queue.put( self.STOP_SIGNAL ) log.info( "pbs job runner stopped" )

- def get_stage_in_out( self, fnames ): + def get_stage_in_out( self, fnames, symlink=False ): """Convenience function to create a stagein/stageout list""" stage = '' for fname in fnames: if os.access(fname, os.R_OK): - if stage != '': + if stage: stage += ',' # pathnames are now absolute - if self.app.config.pbs_stage_path != '': + if symlink and self.app.config.pbs_stage_path: stage_name = os.path.join(self.app.config.pbs_stage_path, os.path.split(fname)[1]) else: stage_name = fname