CASAVA running on PBS pro

[westerman]

As we probably all know, Casava can be made to run in parallel on SGE (sun grid engine). Is it possible to have it use PBS instead? The commands are similar (e.q., qsub, qstat) yet frustratingly different in the option details.

Modifying or adding to:

CASAVA/lib/CASAVA-1.7.0/perl/Casava/TaskManager

should do the trick. But if someone else has already done the modification then I would prefer to use that. BTW, Illumina support only recommends SGE and does not seem to be interested in supporting PBS.

Thanks.

[hpcguy]

There are already some solutions for this for LSF. (search the forum)

I think we had a request for this here recently, I'll see what happened with it. We run torque/Moab so anything we change should be close enough for Altair PBSPro.

It's been a version or two since I looked at it, but CASAVA is really nothing more than an evil elaborate makefile wrapper that uses sgmake. Try using distmake or pmake in it's place. I suspect that will be enough to get you up and running.

hpc

[dejavu2010]

Anyone has update about this post? I have the same problem

[westerman]

I am not using CASAVA with PBS per se. Instead I do the deconvolution on a multi-CPU node and then split up the next processing on a per-sample basis -- one sample per node.

[GenoMax]

You should be able to get CASAVA to work with a queuing engine of your choice with some tinkering. Unfortunately you will be doing this each time a new version of pipeline is released.

Scenario to consider is if you ever run into a problem. To be clear, Illumina tech support is great and they do try to help. But if they determine that the problem is specific to your queuing system then you will need to find a solution on your own.

[User001]

There are already some solutions for this for LSF. (search the forum)

I think we had a request for this here recently, I'll see what happened with it. We run torque/Moab so anything we change should be close enough for Altair PBSPro.

It's been a version or two since I looked at it, but CASAVA is really nothing more than an evil elaborate makefile wrapper that uses sgmake. Try using distmake or pmake in it's place. I suspect that will be enough to get you up and running.

hpc

We're working on installing CASAVA on a cluster using a Torque/Maui scheduler. Does anyone have a good guide for this? hpcguy do you have some advice?

[aunderwo]

Torque and Casava

Hi

Did you have any success with this. We're hoping to do the same.

Thanks

We're working on installing CASAVA on a cluster using a Torque/Maui scheduler. Does anyone have a good guide for this? hpcguy do you have some advice?