details: http://www.bx.psu.edu/hg/galaxy/rev/0edb42925161 changeset: 3014:0edb42925161 user: Nate Coraor <nate@bx.psu.edu> date: Wed Nov 11 15:13:12 2009 -0500 description: The job working directory was not being used for _any_ cluster jobs. No idea how this was missed for so long. Data source jobs should now work on the cluster. diffstat: lib/galaxy/jobs/runners/pbs.py | 4 ++-- lib/galaxy/jobs/runners/sge.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diffs (33 lines): diff -r 120a34362c82 -r 0edb42925161 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 14:57:34 2009 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 15:13:12 2009 -0500 @@ -205,7 +205,7 @@ job_attrs[3].value = stageout job_attrs[4].name = pbs.ATTR_N job_attrs[4].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.path.abspath( os.getcwd() ) + exec_dir = os.path.abspath( job_wrapper.working_directory ) # If not, we're using NFS else: job_attrs = pbs.new_attropl(3) @@ -215,7 +215,7 @@ job_attrs[1].value = efile job_attrs[2].name = pbs.ATTR_N job_attrs[2].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.getcwd() + exec_dir = os.path.abspath( job_wrapper.working_directory ) # write the job script if self.app.config.pbs_stage_path != '': diff -r 120a34362c82 -r 0edb42925161 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Wed Nov 11 14:57:34 2009 -0500 +++ b/lib/galaxy/jobs/runners/sge.py Wed Nov 11 15:13:12 2009 -0500 @@ -143,7 +143,7 @@ if sge_queue_name is not None: jt.setNativeSpecification( "-q %s" % sge_queue_name ) - script = sge_template % (job_wrapper.galaxy_lib_dir, os.getcwd(), command_line) + script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) fh = file( jt.remoteCommand, "w" ) fh.write( script ) fh.close()