is it possible to use a gcs bucket directory as tmp directory?

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joy bordini

• January 07, 2021 19:08

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I was using GATK4.1.4.1 with GenomicsDBImport command and I was wondering if it is already implemented the possibility to use a google cloud storage directory as tmp directory.

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  Genevieve Brandt (she/her)

  • January 08, 2021 21:44

  Hi joy bordini, within our GATK code there is not something already set up to do this. Have you checked out our platform Terra? It uses google cloud buckets for storing data and provides an easy way to run GATK. You can find out more here and I can also connect you with the Terra Support team if you have questions.

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  joy bordini

  • January 11, 2021 12:25

  Dear Genevieve,

   

  Thank you for your reply. I tried to use Terra but it is quite uncomfortable to type all the samples when you have a lot of them. I integrated my gatk pipeline in Snakemake that makes me handle all the diversities of options and samples. I'll try to use it directly on google cloud kubernetes in order to speed the pipeline and use less ram. But of course if there is a way to maintain the module directory organization of snakemake (snakefile, rules/common.smk, reference.smk etc) on Terra I'll be happy to try.

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  Jason Cerrato

  • January 11, 2021 17:34

  Hi joy bordini,

  My name is Jason and I'm one of the Terra Support Specialist. I'm not very familiar with the requirements for snakemake, but I may have some ideas for how you can leverage Terra for ease of running analyses.

  You mentioned that you are having discomfort typing all of the samples. If you workflow is written to handle a directory full of samples, you can consider creating a .tar.gz file that contains all of your samples and feeding it into the workflow, which will be written to extract the contents of the tarball.

  You can also consider setting up the data tables for ease of running analysis on multiple samples, or on a set of samples. You can find documentation for how to do this here: https://support.terra.bio/hc/en-us/articles/360047046131-Data-Tables-QuickStart-Part-1-Intro-to-data-tables-

  And here is a helpful video that explains how to make a table: https://www.youtube.com/watch?v=2MxSlKhIrFY

  If you have any questions, please let me know.

  Kind regards,

  Jason

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