Re: [galaxy-dev] use_tasked_jobs
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<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
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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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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Chorny, Ilya -
Dannon Baker