Re: [svtoolkit-help] Is it possible to install Genome STRiP on an HPC cluster with SLURM as the management software?

[Wusheng Z. <min...@gm...>]

Hi Bob,


Thank you very much for your help! After reading your answer, I found I am
too ignorance to the genomestrip last month, and now I think I have enough
knowledge for asking help. Since the cluster I am using is slurm 17.11.7, I
hope that I can directly use Drmaa without the patches. But if it does not
work, it will be very helpful if you can share your pathces. And I am
trying to persuade the administrator to install the Drmaa now.


But before that, is it possible to run CNVDiscovery sequentially with the
--jobRunner Shell \ --gatkRunner Shell \ (without any --jobnative flag) on
the cluster? BTW, based on my understanding, only to the CNVDiscovery step,
specifying the --jobRunner and --gatkRunner is needed — is this correct?


And should I ask questions on the GATK forum rather than the mailing list?


Thank you very much.


Best regards,

Wusheng


Bob Handsaker <han...@br...> 于2018年5月18日周五 下午5:36写道：

> Hi, Wusheng,
>
> I have gotten Genome STRiP (GS) to run on slurm, but the one time I did
> this we had to make a patch to the DRMAA library. This was done for a
> relatively old version of slurm (that was running on the cluster of
> interest) and although I sent some emails I never got any feedback as to
> whether the patches could be contributed back to the slurm code base.
>
> If you want to try to get it running, I am happy to share the slurm
> patches we had to make with you, especially if you would help get the drmaa
> API fixes to be generally supported in slurm.
>
> -Bob Handsaker
> On 5/18/18 12:38 PM, Wusheng Zhang wrote:
>
> Dear Genome STRiP users,
>
> I am new to this software and intend to install this software on my
> university HPC cluster. But the cluster management software the university
> is using is the SLURM rather than LSF or SGE. In this sense, is it still
> possible to install Genome STRiP on my university cluster and is there
> anything I need to change based on the original installation steps? Thank
> you very much.
>
> Best regards,
> Wusheng
>
>
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