API authentication for terra lab-cli use on HPC

Christina Robinson

January 06, 2026 20:00

Hello, 

 

I'm wondering for individuals that may want to create automated workflows - is there the capability with terra lab-cli to enter details for API tokens to authenticate to your terra account so that jobs could be submitted and retrieved via an automated process?

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  Jose M Soto

  January 12, 2026 19:07

  Hey Christina,

  There is currently no way to automate authenticating to the client without some kind of manual intervention every ~2 weeks as this is when tokens generated by the cli expire.  Within that 2 week period you can authenticate to the service and copy the tokens generated to wherever the terralab cli you are running expects the tokens to be, `$HOME/.terralab` by default, to allow some long running automated process feel like it didn't require intervention but in reality it did.

  Could you tell us more about your use case?  This is probably something that would useful to have for a majority of cli users

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  Christina Robinson

  January 13, 2026 00:48

  I am attempting to create an automated genotyping harmonization, QC, imputation, and global and genetic ancestry estimation nextflow pipeline that has all of us + anvil as an imputation panel option and allow benchmarking of approaches for different populations. I see that some broad features have employed fiss for api access. Is this an option that might integrate with the panel? I believe I can leave instructions to include the tokens in the .config file and update as needed for now but was trying to see if fiss might work to be a bit more automated. 

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  Christina Robinson

  January 13, 2026 00:53

  I’m also curious if aggregate level variant summary data included in the panel or population-specific LD and recombination rates from the panel might be publicly available at some point. These could be potentially be used to improve variant retention and quality for populations of interest.

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  Jose M Soto

  January 13, 2026 20:34

  Thank you for explaining your use case!  FISS uses gcloud to auth so if your environment is able to utilize FISS you should also be able to auth to our cli using terralab login-with-oauth $(gcloud auth print-access-token). This command should allow you to create your automated pipeline how you originally wanted it.  My guess would be that FISS wont be adding our APIs to their cli but it might worth creating an issue to gauge interest.

   

  I have a query out about sharing out some of the summary data you mentioned and will let you know once I get a response.  The only summary data we've made available so far is a sites only vcf of the reference panel that has AF annotation information.  The link can be found at https://broadscientificservices.zendesk.com/hc/en-us/articles/39921694846619-About-the-reference-panel 

   

   

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  Jose M Soto

  January 15, 2026 17:31

  It seems unlikely we would publish the summary metrics you mentioned unless there was a larger interest from users.  If this was something you really wanted, researcher workbench could be used to get most of the underlying data in the panel to calculate those metrics.

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