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

1 comment

  • 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

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