[DOCKTESTERS] Broad PCAWG Tokens definition?

[Gordon Saksena]

Tokens is the only one ready for testing.

Yes, I need to sync the Dockerhub repo with the code updates from GIT.

I am using a debian7bp environment for my builds and testing.

The readme is for creating and debugging new tasks.  Your test environment
is probably going to be quite different.

There is a .tok.gz file included in the Broad intermediate files for each
donor.  The intermediate files currently live on GNOS, in the form of one
tarfile per donor.  Either you can pull it from there, or I could post one
to Jamboree for some donor.

Gordon

On Thu, Oct 20, 2016 at 5:19 PM, Alexander Buchanan <buchanae at ohsu.edu>
wrote:

> I forgot to add: the tokens task is the only part that’s ready for
> testing, correct?
>
>
>
> *From: *<docktesters-bounces+buchanae=ohsu.edu at lists.icgc.org> on behalf
> of Alexander Buchanan <buchanae at ohsu.edu>
> *Date: *Thursday, October 20, 2016 at 2:18 PM
> *To: *Gordon Saksena <gsaksena at broadinstitute.org>
> *Cc: *"docktesters at lists.icgc.org" <docktesters at lists.icgc.org>
> *Subject: *Re: [DOCKTESTERS] Broad PCAWG Tokens definition?
>
>
>
> Great, thanks Gordon.
>
>
>
> Fyi, I just finished a successful run of the tokens wdl with a relatively
> small BAM file. I had to rebuild the docker image, because the one hosted
> on Dockerhub was missing a source file. I filed a github issue for that
> here: https://github.com/broadinstitute/pcawg/issues/10
>
>
>
> A rebuild of the image seemed to do the trick. I had some issues building
> it (now resolved), probably because my build environment was different
> (Mac) and/or broken (mysterious network issues with Bioconductor.org).
>
>
>
> Is there some expected input/output pair I should be using to validate
> that it’s working as expected?
>
>
>
> I don’t have any feedback on the internals of the docker images
> necessarily (pipette, single wdl task, etc). I think my first impression
> was just being a little confused looking at the repo and not knowing where
> to start. The docs mention Firecloud, GCE, make, etc. which doesn’t match
> my environment, so I didn’t easily know where to start. But, after a day or
> poking around I figured it out. I guess that’s to be expected when opening
> up a new codebase on an unfamiliar and unreleased project.
>
>
>
> Thanks again,
>
> Alex Buchanan
>
>
>
> *From: *Gordon Saksena <gsaksena at broadinstitute.org>
> *Date: *Thursday, October 20, 2016 at 2:03 PM
> *To: *Alexander Buchanan <buchanae at ohsu.edu>
> *Cc: *"docktesters at lists.icgc.org" <docktesters at lists.icgc.org>
> *Subject: *Re: Broad PCAWG Tokens definition?
>
>
>
> The tokens task is part of the PoN (Panel of Normals) filter.  It is a
> Java program that collects stats on the Normal BAM for the current donor.
> These stats are later aggregated with stats from the other samples (in
> another docker), and then used to flag certain variants in a VCF as suspect
> (in a third docker).  The overall algorithm is in the process of being
> published.
>
>
>
> It should be one of the more straightforward algorithms to test - it has
> very predictable CPU time and RAM usage, and should produce outputs that
> can be tested via an exact binary match.  It accepts just the normal BAM
> for its input.
>
>
>
> I'm planning later dockers to have a similar structure, though with
> increased memory and core requirements.  The .wdl file will continue to
> contain a single task, with the bulk of the pipeline wiring embedded inside
> the docker.  The dockers will either accept the source BAMs (for callers)
> or VCFs (for filters) as inputs.  If you have feedback I can incorporate it
> into the other dockers.
>
>
>
> Gordon
>
>
>
> On Thu, Oct 20, 2016 at 4:08 PM, Alexander Buchanan <buchanae at ohsu.edu>
> wrote:
>
> Hey Gordon,
>
>
>
> I’m new here so maybe I missed this, but what is the tokens task? How
> would you describe what it does and the results it produces?
>
>
>
> Thanks!
>
> Alex Buchanan
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.icgc.org/mailman/private/docktesters/attachments/20161020/120b34d9/attachment-0001.html>