User

Andrew Davidson

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Recent activity by Andrew Davidson

  • 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

  • output directory is missing? /cromwell_root/script: line 103: 22 Killed salmon quant

    I wrote a workflow that uses Salmon. One of the arguments to salmon is --output, ie the directory salmon will write to. Before calling salmon I call ```mkdir salmon.out``` salmon runs for about 10 ...

    • 2 followers
    • 16 comments
    • 0 votes

  • trick to make bash tasks easier to debug

    FYI Here is a trick so that you can use `set -x`. to create bash script trace of the execution. this can be handy for debugging.  You will see the command and the output in a single file.  enjoy, s...

    • 1 follower
    • 0 comments
    • 1 vote

  • 'task command' how to work with local variables

    I having trouble writing tasks. I think the issue is that you can not simply cut and past bash scripts. This like variable substitution do not work as expected. I wonder if there is some more detai...

    • 3 followers
    • 3 comments
    • 0 votes

  • how can I find my "job cost" is

    Hi  I am working on a proof of concept for my Lab. One of the things I need to do is estimate the cost for a very large workflow. My plan was to run the workflow on a small set of sample and use th...

    • 2 followers
    • 1 comment
    • 0 votes

  • RFE: making it easier to work with files and workflow execution buckets

    I am working through a proof of concept project for my lab. I am very impressed with Terra so far.  I understand the need to name buckets using GUIDs however it is not very human-friendly. Bellow, ...

    • 2 followers
    • 2 comments
    • 1 vote

  • it hard to add new tasks to an existing name space

    I am a newbie. I want to use the namespace like a package in java. that is to say I have several tasks in the same name space when I create a new task it would be much less error prone if there was...

    • 2 followers
    • 4 comments
    • 0 votes