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Old 01-24-2011, 02:28 AM   #1
rdeborja
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Default BFAST submission to SGE script

Has anyone tried the bfast.submit.pl tool to submit jobs to an SGE cluster? If yes, can you provide an example config script?
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Old 02-21-2011, 11:03 PM   #2
Vincenzo
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Dear,
i have the same problem.
Did you solve it?
If yes, please can you shared your script?
I sent an e-mail to the group with object "Bfast parallel running".
Thanks a lot
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Old 02-22-2011, 12:15 AM   #3
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There is no tutorial and it is meant for advanced users. To obtain the XML schema, use the "--schema" command line option. Modify it appropriately (you may need to read the perl script!) making sure you create an XML file too.
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Old 02-22-2011, 10:53 AM   #4
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Hi,

I am trying to run bfast in PBS. The script has to be written in such a way to combine all the steps of bfast into a single PBS script and submit the job. Please help in writing the pbs script to run bfast in cluster computing.
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Old 02-22-2011, 11:23 AM   #5
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Quote:
Originally Posted by Venkat View Post
Hi,

I am trying to run bfast in PBS. The script has to be written in such a way to combine all the steps of bfast into a single PBS script and submit the job. Please help in writing the pbs script to run bfast in cluster computing.
What is your specific question? What have you already tried? Have you created an XML file according to the schema? Do you have a local bioinformatician that can help?
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Old 03-01-2011, 06:03 AM   #6
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Sorry. I do not have a bioinformatician to help. My question is how to run bfast in cluster system. I tried running in local computer it works well with the example. but I am not sure of working with remote cluster machine.
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Old 03-01-2011, 09:14 AM   #7
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Quote:
Originally Posted by Venkat View Post
Sorry. I do not have a bioinformatician to help. My question is how to run bfast in cluster system. I tried running in local computer it works well with the example. but I am not sure of working with remote cluster machine.
It is beyond the scope here to describe how to run such programs on a remote cluster machine. You will need to contact someone who can help (a bioinformatician, a systems administrator, or someone with the requisite knowledge). Your request is similar to me saying I learned to run a PCR, can you now tell me how to do library preparation for my DNA sequencer?
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