1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/958d1f8b2caf/ changeset: 958d1f8b2caf user: Scott McManus date: 2012-06-19 20:10:08 summary: Merge issues. affected #: 2 files
diff -r 22eea899376f142134c30abafb6e156a514574dd -r 958d1f8b2caf9595d79e66d1eb1705110a1a6784 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -310,7 +310,7 @@ # Check exit codes and match regular expressions against stdout and # stderr if this tool was configured to do so. if ( len( self.tool.stdio_regexes ) > 0 or - len( self.tool.exit_codes ) > 0 ): + len( self.tool.stdio_exit_codes ) > 0 ): # We will check the exit code ranges in the order in which # they were specified. Each exit_code is a ToolStdioExitCode # that includes an applicable range. If the exit code was in
diff -r 22eea899376f142134c30abafb6e156a514574dd -r 958d1f8b2caf9595d79e66d1eb1705110a1a6784 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -77,6 +77,7 @@ self.job_file = None self.ofile = None self.efile = None + self.rcfile = None self.runner_url = None
class DRMAAJobRunner( BaseJobRunner ): @@ -168,6 +169,7 @@ # define job attributes ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + rcfile = "%s.drmrc" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) )
@@ -176,6 +178,7 @@ jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile + jt.returnCodePath = ":%s" % rcfile native_spec = self.get_native_spec( runner_url ) if native_spec is not None: jt.nativeSpecification = native_spec @@ -228,6 +231,7 @@ drm_job_state.job_id = job_id drm_job_state.ofile = ofile drm_job_state.efile = efile + drm_job_state.rcfile = rcfile drm_job_state.job_file = jt.remoteCommand drm_job_state.old_state = 'new' drm_job_state.running = False @@ -312,6 +316,7 @@ """ ofile = drm_job_state.ofile efile = drm_job_state.efile + rcfile = drm_job_state.rcfile job_file = drm_job_state.job_file # collect the output # wait for the files to appear @@ -377,6 +382,7 @@ drm_job_state = DRMAAJobState() drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + drm_job_state.rcfile = "%s.drmrc" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job.id) drm_job_state.job_id = str( job.job_runner_external_id ) drm_job_state.runner_url = job_wrapper.get_job_runner()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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