[DOCKTESTERS] Core workflow icgc reference data location and gosu

[Miguel Vazquez]

Francis, I'll rerun the test. I'm still waiting for the Sanger wf test that
has been running for about 10 days. I'll see if it completes by Monday,
 otherwise I'll think if I abort and retest dkfz and see if I can debug
 bwa-mem.

Best

Miguel

On Dec 2, 2016 9:39 PM, "Francis Ouellette" <francis at oicr.on.ca> wrote:

>
> 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> 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
>
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