User: janecao999

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janecao9990
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Posts by janecao999

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Comment: C: sge drmaa cluster galaxy configuration
... Hi Nate, The issue is still existed. Again, the galaxy stopped at self.ds.run_job(**jt) step. we debugged further from there and noticed that "setattr(template,key,kwds[key])" command doesn't work. I also posted the issue in galaxy IRC site. ...
written 23 days ago by janecao9990
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galaxy 18.01 sge drmaa
... The galaxy release 18.01 didn't work with our sge cluster. We tried to trace where the bug can be and noticed that galaxy process stopped when reached "setattr(template, key, kwds[key])" command under .venv/lib/python2.7/site-packages/pulsar/managers/util/drmaa. We used ""template.key = kwds[key]" ...
galaxy written 5 weeks ago by janecao9990
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Comment: C: sge drmaa cluster galaxy configuration
... Hi Nate, I checked drmaa.py (lib/galaxy/jobs/runners) from galaxy and noticed that external_runjob_script was returned as "None" from job_wrapper.get_destination_configuration. Because it is 'None', a while loop to create external_job_id shall be called. But it seems that self.ds.run_job(**jt) is ...
written 6 weeks ago by janecao9990
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Comment: C: sge drmaa cluster galaxy configuration
... when I added webless handler into job_conf.xml file (, run "./scripts/galaxy-main -c config/galaxy.yml --server-name handler1 --daemonize", it exited with "ImportError: Attempted to use Galaxy in daemon mode, but daemonize is unavailable.". I then used uWSGI all-in-one job handling function and add ...
written 7 weeks ago by janecao9990 • updated 7 weeks ago by Nate Coraor3.2k
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Comment: C: sge drmaa cluster galaxy configuration
... After native specification, I didn't see "queued as #id". I can use "qsub" in command line to submit jobs without any problems. I also turned on the heatbeat.log in galaxy.yml file, but the logs just gave me a bunch of traceback dump for each main.web threads and it doesn't seem contain any specif ...
written 7 weeks ago by janecao9990
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Comment: C: sge drmaa cluster galaxy configuration
... The galaxy.yml was configured as uWSGI all-in-one job handling. All job logs should be sent to galaxy.log file. I checked the log file and the job associated with tophat has log as: galaxy.jobs DEBUG 2018-05-02 19:05:11,320 [p:26594,w:1,m:0] [JobHandlerQueue.monitor_thread] (31) Working directory ...
written 7 weeks ago by janecao9990
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Comment: C: sge drmaa cluster galaxy configuration
... Hi Nate, Where can I define job handler? In the old version of galaxy, I defined job handlers in universe_wsgi.ini file with definition as: [server:handler0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = True threadpool_workers = 8 [server:handler1] use = egg:Paste#http port ...
written 7 weeks ago by janecao9990
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sge drmaa cluster galaxy configuration
... I recently installed a local galaxy. I want to distribute jobs to local (as default and run in headnode) or to a sge cluster. The job_conf.xml was configured as: 2 ...
drmaa job_conf.xml galaxy sge admin written 7 weeks ago by janecao9990 • updated 7 weeks ago by Nate Coraor3.2k
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Comment: C: galaxy local installation
... I created job_conf.xml file and make local as default and a few alignment programs to run in cluster (sge_default). The jobs submitted to default/local worked well, but jobs to sge_default cannot be pushed to queuing system. The job_conf.xml is: ``` ...
written 7 weeks ago by janecao9990 • updated 7 weeks ago by Martin Čech ♦♦ 4.7k
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Comment: C: galaxy local installation
... Issue solved after comment out lines. Thanks a lot, Martin! ...
written 7 weeks ago by janecao9990

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