Re: [galaxy-dev] Galaxy with PBS runner Setting
On Dec 20, 2011, at 12:19 AM, Le-Shin Wu wrote: Thanks a million, Nate. I was able to submit my PBS job though galaxy. But I got another problem once the PBS job is finished. I submit a bowtie alignment testing job to our cluster by using PBS runner through galaxy. But I always got an error message showing on the right history panel as below. An error occurred running this job: # reads processed: 17214026 # reads with at least one reported alignment: 16405756 (95.30%) # reads that failed to align: 808270 (4.70%) Reported 16405756 alignments to 1 output stream(s) In fact, the message showing here is the output message from bowtie application and I did get the correct alignment result stored on galaxy server machine. Therefore, I tried adding some PBS options, such as -k eo or -j eo -o /dev/null, to the PBS runner in universe_wsgi.ini to remove the standard output message from bowtie. But this time I got the following error message. Hi Le-Shin, I am not familiar enough with bowtie to know why this error occurred. Perhaps someone else on the list can reply with some information. Please keep replies on the mailing list to ensure this is possible. An error occurred running this job:Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. It looks like if galaxy PBS runner did not receive the standard output from cluster, it will throw an error. Could you please help us to solve this problem. Thanks a lot. That's correct, Galaxy controls the location of the stdout/stderr files, changing these will cause such failures. --nate Le-Shin ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy with PBS runner Setting
On Dec 19, 2011, at 3:03 PM, Le-Shin Wu wrote: We are trying to get galaxy to work on our cluster. Unfortunately, there are some questions I still cannot find the answer to and I'm hoping someone here can help me out. We would like to use the unified approach with TPRQUE PBS to support running galaxy tools on a cluster. Our questions are listed as below. (1) How to configure the universe_wsgi.ini file? Based on the galaxy wiki page, we changed the following parameters in universe_wsgi.ini new_file_path = /N/dc/projects/galaxy/new_files # this directory is accessible both to galaxy server and cluster nodes start_job_runners = 'pbs' default_cluster_job_runner = pbs://cluster.hostname.edu/ #cluster.hostname.edu is the hostname for our cluster Also under [galaxy:tool_runners] section, we add a new tool named mytool for testing as below. mytool = pbs://cluster.hostname.edu/ Does this configuration look correct and enough? (2) We created a new python egg for pbs by using LIBTORQUE_DIR=/usr/local/lib/libtorque python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini A new file pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg was then created under eggs. Do we need to do other things or only this operation is enough? (3) We created a new directory named mytool under tools and added a new file named newTool.xml in it. The content of newTool.xml is as below. Note that, the /N/soft/mason/test_tool is a executable binary file at our cluster. tool id=mytool name=Testing tool version=0.12.7 descriptiondo the pbs testing/description command /N/soft/mason/test_tool -p 8 hg18 -f $inputseq $output /command inputs param name=db type=inputseq label=input file / /inputs outputs data format=sam name=output label=result / /outputs tests test param name=inputseq value=a.fa / output name=output file=b.sam / /test /tests help **What it does** This tool uses Bowtie to produce an alignment. .. _Bowtie: http: /help /tool Does this xml file look correct? Do we also need a python wrapper file to somehow invoking PBS support? (4) Add the following text into tool_conf.xml. section name=My Tools id=mt tool file=mytool/newTool.xml / /section (5) After doing the above modification and restarting our galaxy server , we can see My Tools showing on the tools panel of our galaxy web interface. But after we select an input file and click execute button, the job status shows an error Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. We also check the log file, it shows Invalid job runner: bps. Hi Le-Shin, It would appear that the PBS job runner failed to start. You should be able to see a traceback with more details about this displayed during the server's startup. --nate We appreciate very much for your kind help. Le-Shin ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
