[DOCKTESTERS] SV Merge image in Dockstore

[Denis Yuen]

Hi,


As mentioned in the Monday call, I took a quick look at https://dockstore.org/containers/registry.hub.docker.com/essi/pcawg_sv_merge <https://bitbucket.org/weischenfeldt/pcawg_sv_merge>

It looks like the tool is functional and I was able to run it with the test data (a small test json is registered on dockstore and is available here https://bitbucket.org/weischenfeldt/pcawg_sv_merge/src/26bcbf6b86935417d8be5a379b3657167076c6b8/Dockstore.json?at=docker&fileviewer=file-view-default )

A couple heads-up though:
1) It appears that there's a bug with version 1.1.5 of Dockstore where it looks like Dockstore does not copy the results to the final location and instead leaves them in place when working with array output. This means that for now, users will need to look at the stdout file which does list all the output files (the file will be at a path that looks like ( <your working directory>./datastore/launcher-6dd9b514-fe37-4290-8f36-5fb28e5a7f3a/outputs/cwltool.stdout.txt )
2) I wasn't able to download the full Synapse dataset, but this may be an issue with my account since the underlying dataset seems to be hosted at dccsftp.nci.nih.gov rather than Synapse itself. Link is available here https://www.synapse.org/#!Synapse:syn8547037

In short, I believe that the tool should be ready for testing although there are a couple rough edges to work on (although they shouldn't block testing).



Denis Yuen
Senior Software Developer

Ontario Institute for Cancer Research
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