[DOCKTESTERS] Core workflow icgc reference data location and gosu

[Alexander Buchanan]

I don’t think we’ll have time before Monday morning to run any of the new containers.

I’ll probably try out the new dkfz container early next week though, as I have been having lots of issues with running DKFZ on Cromwell. The issues are related to read-only files being mounted and dkfz switching users to “roddy”, so I’m hoping the gosu changes will help.

From: <docktesters-bounces+buchanae=ohsu.edu at lists.icgc.org> on behalf of Francis Ouellette <francis at oicr.on.ca>
Date: Friday, December 2, 2016 at 12:39 PM
To: "docktesters at lists.icgc.org" <docktesters at lists.icgc.org>
Subject: Re: [DOCKTESTERS] Core workflow icgc reference data location and gosu


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
MaRS Centre
661 University Avenue
Suite 510
Toronto, Ontario, Canada M5G 0A3
Toll-free: 1-866-678-6427
Twitter: @OICR_news
www.oicr.on.ca<http://www.oicr.on.ca/>
This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
_______________________________________________
docktesters mailing list
docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>
https://lists.icgc.org/mailman/listinfo/docktesters

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.icgc.org/mailman/private/docktesters/attachments/20161203/fc23faf0/attachment-0001.html>