[DOCKTESTERS] Broad dockers

[Gordon Saksena]

Hi,

I have approval for the Broad PCAWG dockers to go on the staging
(non-password protected) portion of Dockstore.  The Github Repo and
DockerHub image have permissions granted to folks who sent me their github
and docker usernames.  This should be adequate for the initial rounds of
testing.

The tokens portion of the pipeline should be ready for folks to give it a
spin.  The non-protected reference files are passed in via http in the
inputs file, and it only needs the normal BAM.  It takes about 5 hours on a
full size file using a couple cores.  Other portions will be added as they
are split out and tested.

While the current permissions setup is fine for testing, something
different will be needed for post publication.  Many of the algorithms are
(or will be) free only for educational or research use, but require a
separate license for commercial use.  We should discuss how that use case
can be supported, and whether it has implications on testing.


https://hub.docker.com/r/broadinstitute/pcawg_tokens/

https://github.com/broadinstitute/pcawg
https://github.com/broadinstitute/pcawg/blob/master/tasks/tokens/taskdef.tokens.wdl
https://github.com/broadinstitute/pcawg/blob/master/tasks/tokens/inputtest_http_refdata.tokens.json

Gordon
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