[DOCKTESTERS] Core workflow icgc reference data location and gosu

[Francis Ouellette]

OHSU people: any chance some of these will be tested before Monday AM’s call?

Miguel: Can you rerun some of your successful tests with this new dockstore?

All: any testing possible?

Gordon: What is up with broady docker containers?

We also have a request from Peter van Loo, to join this group — I said yes, but he wants to test other containers from his group … Which is great!

After I get some specifics from him I will add peter and other(s) from his group.

Stay tuned,

Also, please update things on wiki/google doc as you progress forward,

Thank you,

@bffo


--
B.F. Francis Ouellette          http://oicr.on.ca/person/francis-ouellette








On Dec 2, 2016, at 12:15 PM, Denis Yuen <Denis.Yuen at oicr.on.ca<mailto:Denis.Yuen at oicr.on.ca>> wrote:

Hi,

I've gone through and created a new release for each of the core tools (bwa-mem, delly, dkfz, sanger) with two (non-scientific) changes.

1) Each of these tools has been redirected to use reference data hosted on the icgc portal ( https://dcc.icgc.org/releases/PCAWG ) rather than aws in order to conserve our use of S3. This means that sample json parameter files have been updated and any references inside the Docker images that we're aware of also have been updated. As usual, if re-running workflows frequently, you'll want to host these files locally.

If you are using the Dockstore command-line interface, you'll need to upgrade to the latest release of dockstore (1.2) to use this new file location.

2) A number of users have run into problems running the workflow when running in a multi-user environment (i.e. not running Docker containers with the first user on a host). This release replaces most usage of sudo inside the tools with gosu to deal with this issue.

The new release numbers are documented at https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data
In particular:

  *   bwa-mem 2.6.8_1.2
  *   dkfz 2.0.1_cwl1.0
  *   sanger 2.0.3
  *   embl 2.0.1-cwl1.0


Denis Yuen
Bioinformatics Software Developer

Ontario Institute for Cancer Research
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