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:dannonba...@me.com]
Sent: Friday, September 23, 2011 4:18 AM
To: Chorny, Ilya
Cc: Nate Coraor (n...@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" <dannonba...@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: icho...@illumina.com
>>> Website: www.illumina.com
>>>
>>>
>>> ___________________________________________________________
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>>>
>>> http://lists.bx.psu.edu/
>>
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