Troubleshooting MCMICRO on O2

The following are common problems users encounter on O2. For more information, please review the instructions for running MCMICRO on O2.

I am getting java: command not found

Make sure Java is loaded by doing module load java

I am getting docker: command not found

Be sure to include -profile O2 if you are in the lsp group on O2 and -profile O2ext if you are not. Type groups to check if you are in the lsp group.

I am getting FATAL: singularity image is not in an allowed configured path

Rerun nextflow run labsyspharm/mcmicro/setup/O2ext.nf