User: balaszone

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balaszone60
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Posts by balaszone

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Answer: A: How to purge histories from local instance galaxy interface
... OK. They were not marked as permanently deleted since I was not sure how to do that. However, now searching another post, I was able to find that(had to modify galaxy.ini script to turn purge access True) and then permanently delete it. Ran the clean-up scripts. Recalculated disk usage All files ...
written 12 months ago by balaszone60
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How to purge histories from local instance galaxy interface
... Hi, I would like to know how to purge the deleted histories from galaxy interface. I'm running a local instance of galaxy and after running several analysis, Galaxy indicates I'm "Using ~800GB". I deleted all the histories manually and that didnot help. I tried to purge using the commands given in ...
galaxy written 12 months ago by balaszone60
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switching between local node and cluster nodes
... Hello, I have setup a workflow in galaxy and I have modified my job_conf.xml file to queue these jobs in our sge cluster. It runs fine however couple of tools doesnot run as it is supposed to. For eg. makeTagDirectory.xml doesn't produce outputs in the path provided when run in cluster however it ...
galaxy written 14 months ago by balaszone60
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Running multiple workflows with multiple inputs
... Hi, I recently learnt to create workflows and to script in galaxy using bioblend. Seems like a very useful method to automate the analysis. however, I'm trying to batch process workflow(s) with multiple inputs. i.e for example Step 1: yields fastq files for 8 samples in an experiment. Each sample ...
galaxy multiple-inputs workflow written 15 months ago by balaszone60 • updated 15 months ago by Martin Čech ♦♦ 4.2k
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Answer: A: unable to find libdrmaa.so
... Finally able to find it with the help of sys admin. I had to use the one under the ../UGE folder and not ../SGE for some weird reason. ...
written 15 months ago by balaszone60
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Comment: C: Galaxy not starting correctly - pbs_python error?
... hi, thanks for your quick reply. I did find the location of the file and set the environment variable accordingly. However, now I'm getting a different error when starting galaxy. > DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host "master.cm.cluster" Any thou ...
written 15 months ago by balaszone60
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unable to find libdrmaa.so
... Hi, I'm still having issues configuring galaxy to submit jobs in cluster. Looks like jobs are generally queued using SGE in our cluster. So, I'm trying to configure galaxy to submit jobs via SGE. I'm trying to set a DRMAA_LIBRARY_PATH but unable to locate the libdrmaa.so file as indicated in WIKI ...
drmaa galaxy cluster admin written 15 months ago by balaszone60 • updated 15 months ago by James Taylor470
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Comment: C: Galaxy not starting correctly - pbs_python error?
... Hi, Pardon my lack of knowledge in understanding this installation. Is libtorque part of some application? I have installed the latest version of Galaxy assuming everything should have been updated. Also, WIKI suggested this compilation :- LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.p ...
written 15 months ago by balaszone60
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Comment: C: Galaxy not starting correctly - pbs_python error?
... And how do I that? Can I update without root permissions? Tx ...
written 15 months ago by balaszone60
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Comment: C: Galaxy not starting correctly - pbs_python error?
... Can anybody help with the pbs_python installation error especially with this newer version of Galaxy. All the WIKI docs reflect instructions for older version and i doesnt help much. I read that eggs have been replaced with wheels in this newer version and not sure how one would go about the pbs_py ...
written 15 months ago by balaszone60

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