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

[Denis Yuen]

Hi,
Sorry, catching up with the thread after thanksgiving.

For debugging the state of the filesystem, you can instruct Dockstore to leave the filesystem in place after execution. You can subsequently start the container interactively and examine it.

 The documentation is here https://github.com/ga4gh/dockstore-ui/commit/b3fe88d706da59e6af350ff1dec9d9492a690724 but in short, you need to add `cwltool-extra-parameters: --leave-container`to your config.

For the bas files, Keiran, do you have any thoughts on how this functions differently between the test data and the donor Miguel is using? From the code snippet https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/src/main/java/io/seqware/pancancer/CgpSomaticCore.java#L769-L780<https://webmail.oicr.on.ca/owa/redir.aspx?REF=fliLhQL1K5STxPd-1ApDZRhtddKlatekf0suF2qrynCMdSag4vHTCAFodHRwczovL2dpdGh1Yi5jb20vSUNHQy1UQ0dBLVBhbkNhbmNlci9DR1AtU29tYXRpYy1Eb2NrZXIvYmxvYi9kZXZlbG9wL3NyYy9tYWluL2phdmEvaW8vc2Vxd2FyZS9wYW5jYW5jZXIvQ2dwU29tYXRpY0NvcmUuamF2YSNMNzY5LUw3ODA.> it looks like the bas files are generated from the bam files. Miguel, I would try to to look for that resulting bas file after saving the filesystem as above and see if there appears to be anything wrong with it.




Denis Yuen
Bioinformatics Software Developer

Ontario Institute for Cancer Research
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________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [miguel.vazquez at cnio.es]
Sent: October 11, 2016 8:47 AM
To: Keiran Raine
Cc: docktesters at lists.icgc.org
Subject: Re: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

Hi Keiran,



On Tue, Oct 11, 2016 at 2:40 PM, Keiran Raine <kr2 at sanger.ac.uk<redir.aspx?REF=KcNownvbPs4UQA-6nvkDaABjxnk60l6YSPDuNmlbXpqQUuSo5fHTCAFtYWlsdG86a3IyQHNhbmdlci5hYy51aw..>> 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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