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Use cluster_files_directory for SGE/DRMAA instead of the hardcoded database/pbs/. Fixes issue #512 (thanks, Anonymous).

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This commit is contained in:
Nate Coraor
2011-04-08 09:45:38 -04:00
parent 8f042a795b
commit 7125edcc0a
2 changed files with 4 additions and 4 deletions
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lib/galaxy/jobs/runners/drmaa.py
+2 -2
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@@ -145,8 +145,8 @@ class DRMAAJobRunner( BaseJobRunner ):
job_wrapper.change_state( model.Job.states.QUEUED )
# define job attributes
ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.get_id_tag())
efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.get_id_tag())
ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
jt = self.ds.createJobTemplate()
jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag())
jt.outputPath = ":%s" % ofile
lib/galaxy/jobs/runners/sge.py
+2 -2
View File
@@ -188,8 +188,8 @@ class SGEJobRunner( BaseJobRunner ):
sge_extra_params = self.determine_sge_tool_parameters ( runner_url )
# define job attributes
ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.job_id)
efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.job_id)
ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
jt = self.ds.createJobTemplate()
jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.job_id)
jt.outputPath = ":%s" % ofile