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

[Francis Ouellette]

Brian/Dennis:

Suggestion for a tool/container:

Additional documentation (in readme.md?): checklist of which files need to be there/contributed to the existing container to make the pipeline work.

@bffo


On Oct 11, 2016, at 8:47 AM, Miguel Vazquez <miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:

Hi Keiran,



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