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Former User of DNAx Community_41

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Recent activity by Former User of DNAx Community_41

  • Importing functions from one Jupyter notebook (or Python script) to another within a DNAnexus JupyterLab session

    Hi! I have a number of Python functions that I've written and wish to import into multiple Jupyter notebooks to avoid copy-and-pasting those function definitions repeatedly. Normally, I would just ...

    • 3 followers
    • 9 comments
    • 0 votes

  • Downloading or searching job logs -- where are they?

    Hi! I am trying to search through all the job logs for jobs with a specific tag to see which ones threw a specific warning in stderr. Is there a way to do this more efficiently than navigating to e...

    • 2 followers
    • 2 comments
    • 0 votes

  • Trouble using $in_prefix and $in_name with swiss-army-knife

    Hi! I'm hoping to set up a batch job to extract filters from the vcf files stored atBulk/Exome sequences_Alternative exome processing/Exome variant call files (gnomAD) (VCFs)/. I've been testing ou...

    • 1 follower
    • 2 comments
    • 0 votes

  • gzip can't be run in aws:eu-west2?

    Hi, I was wondering if anyone has found a way to compress generated files on the Research Analysis Platform using gzip. When I try to run "dx run gzip," I get the error: dxpy.exceptions.InvalidStat...

    • 1 follower
    • 1 comment
    • 0 votes

  • Working with Hail outside of JupyterLab

    I've been working on developing pipelines to filter and re-format UKB exome data using Hail. So far, I've been working exclusively in JupyterLab within notebooks by reading in one WES VCF file (fil...

    • 2 followers
    • 4 comments
    • 0 votes

  • ConnectionPoolTimeoutException while working in JupyterLab

    Hello! I've been working on developing a QC and filtering pipeline for UKB exome data using Hail on JupyterLab. For the past two operations I've tried to run, I've received a "ConnectionPoolTimeout...

    • 2 followers
    • 3 comments
    • 0 votes

  • JupyterLab Server Connection Error

    In the past couple of days, I've been getting a server connection error pop up about two hours into any JupyterLab session I start on the RAP. Once I get the error for the first time, I usually fin...

    • 3 followers
    • 8 comments
    • 0 votes