Is there any way to merge the functionality of "Swiss Army Knife" and "Cloud Workstation"?
Specifically, we would like to be able to run do the following (interactively over ssh):
- Access files through /mnt/project/ (dxfuse)
- Use standard genomics tools (e.g., samtools, plink, etc.)
- Upload files to project storage (dx upload)
By ssh-ing into a Swiss Army Knife job, we can do 1. + 2. interactively but not 3. (which produces an error message indicating that UPLOAD is disabled). Cloud Workstation lets us do 3. but not 1. (which seems to be disabled) or 2.
Interesting question ? I think that SAK's "asset" is quite useful for bioinformatician to reuse outside of SAK's applet design. As far as i know, SAK does not have write access to the parent project.
What I would do in this case? I would go either with ttyd or JupyterLab (1 & 3) and run standard genomics tools using dockerized tools / or install dependencies and then save snapshot (2) instead of running SAK "interactively" (which is not actually the intended use case of SAK).
Also I can imagine the situation when I run JupyterLab Terminal and execute "dx run swiss-army-knife" from there. This will produce the results noninteractively, so I can later use it in my downstream interactive analysis.
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Thanks very much for the suggestions. We will continue experimenting with the platform and see which approach works best for our workflows.
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Hello!
Interesting question ? I think that SAK's "asset" is quite useful for bioinformatician to reuse outside of SAK's applet design. As far as i know, SAK does not have write access to the parent project.
What I would do in this case? I would go either with ttyd or JupyterLab (1 & 3) and run standard genomics tools using dockerized tools / or install dependencies and then save snapshot (2) instead of running SAK "interactively" (which is not actually the intended use case of SAK).
Also I can imagine the situation when I run JupyterLab Terminal and execute "dx run swiss-army-knife" from there. This will produce the results noninteractively, so I can later use it in my downstream interactive analysis.
Thanks very much for the suggestions. We will continue experimenting with the platform and see which approach works best for our workflows.
Follow-up question on this: in ttyd, I'm not able to use dx-create-snapshot. Is it possible to create snapshots on a ttyd instance?
I believe that this is not possible from within ttyd.
good to know. thank you!
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