From 7125edcc0af64eb3268232feed7aa349263bbbe9 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Fri, 8 Apr 2011 09:45:38 -0400 Subject: [PATCH] Use cluster_files_directory for SGE/DRMAA instead of the hardcoded database/pbs/. Fixes issue #512 (thanks, Anonymous). --- lib/galaxy/jobs/runners/drmaa.py | 4 ++-- lib/galaxy/jobs/runners/sge.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 7377f33212b..9a523aedf19 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -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 diff --git a/lib/galaxy/jobs/runners/sge.py b/lib/galaxy/jobs/runners/sge.py index 7ab84ff0d20..18b36fc8a41 100644 --- a/lib/galaxy/jobs/runners/sge.py +++ b/lib/galaxy/jobs/runners/sge.py @@ -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