Error: Unable to access jarfile path/to/googlebucket/tool.jar

Post author
Emmalyn Chen

I'm currently trying to run a workflow in Terra with the tool fgbio, which I was able to build and run locally. I copied the jar file to the google bucket associated with the workspace using the command line `gsutil -m cp path/to/jar gs://bucket/location`, but am running into the error `Error: Unable to access jarfile gs://fc-6528258c-9cd6-4c11-abb6-7ffcb8876685/fgbio-0.9.0-0dda145-SNAPSHOT.jar`. Is it because I'm setting an input variable as a path to the jar file in a google bucket? 

I am also running into this error for picard, which I'm also setting as an input variable `picard_jar` to `gs://bucket/picard.jar`. I didn't have this issue with another workflow when I used the docker `us.gcr.io/broad-gatk/gatk:4.1.0.0` and called picard as `/usr/gitc/picard.jar` Do I need to include the jarfile in the gatk docker?

Thanks!

Comments

1 comment

  • Comment author
    Sushma Chaluvadi
    • Edited

    Hi Emmalyn,

    Yes, any software dependencies that you need to run your Workflow need to be in your docker. The docker image is read in per task so if the picard or fgbio is not present in the docker, the workflow will not work. When picard was called as /usr/gitc/picard.jar that is probably because that is the path to picard in the Docker container.

     

     

    0

Please sign in to leave a comment.