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Andrew Davidson

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Recent activity by Andrew Davidson

  • TCGA workspace data sample data dictionary is missing

    I am working with the 33 TCGA controlled access workspaces. The 'sample' data model has 39 features (i.e. columns). I need to quantify the original RNA reads, including the unmapped reads using a n...

    • 2 followers
    • 3 comments
    • 0 votes
    • Answered

  • example of how to set java max heap size dynamically

    If your command runs a java program, increase the runtime memory will probably fix 'out of memory' error. The example shows how to dynamically calculate the max heap size on linux based docker imag...

    • 1 follower
    • 0 comments
    • 1 vote

  • Why are broad institute billing accounts associated with my GCP billing account?

    Hi I recently burned through all my $300 free GCD dollars and am in the process of setting up a new project. My only project is ‘test-aedavids-proj’. When I logged into GCP billing see several othe...

    • 2 followers
    • 2 comments
    • 0 votes

  • how to re-run workflows when some samples fail?

    I have a fairly simple workflow with 2 tasks. The second task depends on the output produced by the first. If I look at the output tab on the workspace workflow tab I see the output is configured c...

    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • how clean up a test workspace?

    I cloned a workspace for testing purposes.  I submitted a bunch of workflows over and over again on the same data set to test performance I would like to get rid of all the "leaked" storage associa...

    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • what does status running mean?

    I running some performance tests today to explicitly understand what happens when I exceed my CPU quota. I was surprised to see the job history page shows the status of all data entries as running?...

    • 2 followers
    • 1 comment
    • 0 votes

  • trouble selecting data sub set

    I am doing a lot of usability, performance, and scaling testing. So far my preliminary results look promising.  I stumbled upon "an ease of use, usability issue" My workspace has a 'samples' table ...

    • Edited
    • 2 followers
    • 4 comments
    • 0 votes

  • Unable to determine when quota has been exceeded

    I think I based my task off of an deprecated example. premptive is a boolean. the example I used defaulted to "3"   I will re-run test and update this request accordingly Andy   I have run some sim...

    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • scaling terra: threads vs CPU how to set quota

    I am trying to figure out how to run big job on terra. I want to be fast, efficient, and cheap. My goal is to create an easy-to-use pipeline for my lab.  many bioinformatic tools allow you to speci...

    • 2 followers
    • 3 comments
    • 0 votes

  • best practices for running large data sets

    I am running a prototype to see if how my lab can use terra.  I ran a small test and found that it took about 6 hrs to run our pipeline on 10 samples. We use preemptible containers. Overall the cos...

    • 2 followers
    • 3 comments
    • 0 votes