BFAST submission to SGE script

[rdeborja]

Has anyone tried the bfast.submit.pl tool to submit jobs to an SGE cluster? If yes, can you provide an example config script?

[Vincenzo]

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

[nilshomer]

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.

[Venkat]

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.

[nilshomer]

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?

[Venkat]

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.

[nilshomer]

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?