gnomad

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Beau Hilton

• October 15, 2020 19:25

I would like to use the python library gnomad to access gnomAD data for use in Hail. It does not appear that this library works with the current Hail environment available within Terra.

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  Jason Cerrato

  • October 15, 2020 20:29

  Hi Beau,

  Thank you for your request! I'm happy to pass this request along to our notebooks team.

  For now, you can use a startup script with these contents for your runtime to get it working:

  #!/usr/bin/env bash

  pip uninstall -y enum34
  pip install gnomad

  I created a notebook with this startup script and found that the package works.

  

   

  You would put the path for where your script lives in the Startup script box.

  

   

  Kind regards,

  Jason

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  Jason Cerrato

  • July 06, 2021 14:59

  Hi Beau Hilton,

  Just wanted to let you know that the gnomad package is now available by default in the Hail configuration.

  Kind regards,

  Jason

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