-
Notifications
You must be signed in to change notification settings - Fork 9
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
test data - 2 #5
Comments
Warning, this takes around 24 hours to run to failure and a pretty beefy machine |
I think I have encountered this error before when I was developing the WDL version... It occurred when the .Rprofile file wasn't being loaded by R because I had changed the home directory. |
I wonder if this means the |
what was the resolution to the issue? |
It turns out cwltool replaces the contents of the working directory when running a docker container. Since that is where the .Rprofile file lives, it gets wiped out resulting in the error above. So we simply create that file anew in the working directory which seems to do the trick. Using a bigger and beefier machine handled the other issue which I suspect was just an out of space error that one of the underlying tools reacted to as a division by zero error. Otherwise, the rest of the changes are just minor syntax changes for CWL 1.0. |
Currently attempting to execute the workflow with the test data on the branch https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/tree/feature/cwl1
Command is
which becomes
Looking at
https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/Dockstore_cwl.json
corresponds to
https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/feature/cwl1/test2.json
Currently fails with the following messages
The text was updated successfully, but these errors were encountered: