1. Terra Support
  2. Platform-wide (security, status and updates)
  3. Release Notes

May 4, 2020

Allie Hajian

The following release notes correspond to the dates April 29, 2020 to May 4, 2020

Interactive Analysis (Notebooks)

New images!

  • Updated all python-derived Terra images to compile pysam with Google Cloud support. This allows pysam to access GCS objects directly without having to first localize to the runtime.

  • Refactor around CRAN and Bioconductor system dependencies for all images that have R dependency (terra-docker-r, terra-docker-gatk, terra-docker-bioconductor)

Workflows, Google integrations and UI

This release includes back-end updates to workflows, Google integrations, and the UI, to improve upcoming features.

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Comments

2 comments

  • Comment author
    Eric Minikel

    This article states "Updated all python-derived Terra images to compile pysam with Google Cloud support. This allows pysam to access GCS objects directly without having to first localize to the runtime" — can you clarify exactly how this is supposed to work? Simply trying:

    samfile = pysam.AlignmentFile("gs://bucket/mybam.bam", "rb")

    results in:

    Failed to open file "gs://bucket/mybam.bam" : Permission denied
    0
  • Comment author
    Ray Jones

    Resurrecting a dead thread to say that adding this before the call to pysam.AlignmentFile() worked for me:

     

    import os, subprocess
    os.environ['GCS_OAUTH_TOKEN'] = subprocess.check_output('gcloud auth application-default print-access-token', shell=True).decode().strip()
    0

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