Thanks. I'm not aware of anyone that's actually tried the basic splitting with drmaa, so this is quite useful. I'll patch central. -Dannon On Sep 23, 2011, at 4:42 PM, Chorny, Ilya wrote:
We also had to make some changes to drama.py so the use_tasks_jobs behaves nicely with drama.
# define job attributes - 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) + ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) + efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile @@ -424,7 +425,7 @@ """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string. Path is hard-coded, but it's no worse than other path in this module. Uses Galaxy's JobID, so file is expected to be unique.""" - filename = "%s/database/pbs/%s.jt_json" % (os.getcwd(), job_wrapper.job_id) + filename = "%s/database/pbs/%s.jt_json" % (os.getcwd(), job_wrapper.get_id_tag()) data = {} for attr in DRMAA_jobTemplate_attributes: try:
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, September 23, 2011 4:18 AM To: Chorny, Ilya Cc: Nate Coraor (nate@bx.psu.edu); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] use_tasked_jobs
TaskWrapper should inherit it from JobWrapper, so I just removed the (unimplemented, other than the pass) overriding TaskWrapper.user property that was preventing that.
On Sep 23, 2011, at 7:11 AM, Chorny, Ilya wrote:
I found it as well. You just copied the user logic from JobWrapper to TaskWrapper?
Sent from my iPhone
On Sep 22, 2011, at 8:39 AM, "Dannon Baker" <dannonbaker@me.com> wrote:
The problem was caused by an unimplemented method in the TaskWrapper. I've fixed it in changeset 6026:3f926d934d98.
-Dannon
On Sep 20, 2011, at 6:58 PM, Chorny, Ilya wrote:
Hi Nate,
We are having an issue that when use_tasked_jobs = True, the job_wrapper.user = None in drama.py. Do you know why that might be. It crashes my code.
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com Website: www.illumina.com
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