links for Singularity and Cromwell

ohlordwhy.md

Quick Links

These are some quick links for the singularity work for Cromwell! Because slack + markdown == pain

• here is the container recipe
• docs for building and running
• the backend configuration with a struggle bus for me to get a PID for the running container :P
• singularity workflow opts (must build container locally since not on Shub!
• possible avenue to get singularity in singularity

I just added one more runtime configuration - that will start and execute a command to an instance instead. This might be an easier avenue to get a process id (e.g., singularity instance list but it still seems to run ok, and exit without any obvious error, so please take a look! The command for the instance run would be:

$ java -jar -Dconfig.file=backends/backend.conf -Dbackend.default=singularity-instance cromwell-34.jar run runners/test.wdl -i data/TEST-YEAST/inputs.json -o workflow_opts/singularity.json

And it uses the same container, but as an instance (singularity-instance is the backend.conf section)