[DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

[Miguel Vazquez]

Hi Keiran,



On Tue, Oct 11, 2016 at 2:40 PM, Keiran Raine <kr2 at sanger.ac.uk> wrote:

> Hi,
>
> There is a step generating the BAS files:
>
> [2016/10/10 07:28:37] |  Running command: bash /datastore/oozie-6599f0b9-
> 8af7-44ca-a608-03c5bbc159c6/generated-scripts/s58_
> basFileGenerate_control_11-runner.sh
> [2016/10/10 07:28:37] |  Running command: bash /datastore/oozie-6599f0b9-
> 8af7-44ca-a608-03c5bbc159c6/generated-scripts/s58_
> basFileGenerate_tumours_12-runner.sh
>
> But if the BAM files and BAS aren't co-located then you have a problem.
> You could symlink the BAM files into the work space and have all tools work
> from that path instead, deleting the symlinks at the end.
>

I'm afraid that this is not under my control. Since I'm running this
through dockstore there is little I can do about it as far as I understand
it.

Maybe someone that knows dockstore can help out at this point?

Best

Miguel
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