Singularity

[austinchipps]

Hello! I'm trying to pull the Docker container from Docker Hub using Singularity (my university HPC doesn't allow the use of Docker). I ran: singularity build roadies.sif docker://ang037/roadies:latest

and it seems to have successfully built "roadies.sif".

I would next like to test ROADIES with the test dataset, but it's unclear how to do so. I manually installed the data from Github and then ran: singularity exec -B /work/.../roadies_dir roadies.sif run_roadies.py --cores 64

and get the message that "run_roadies.py cannot be found in $PATH"

The documentation is unclear as to how Docker/Singularity are used to run ROADIES.

Thank you in advance for your help - look forward to using this tool!!

[ang037]

Thanks for letting us know. I am not aware of the exact commands for Singularity, but you are first required to pull and run the Docker image.

singularity pull ang037/roadies:latest
singularity run ang037/roadies:latest

After this, once you see the roadies_envenvironment activated, you are ready to run our tool (you do not need to clone the ROADIES GitHub repo manually). To run our ROADIES pipeline, first, configure the parameters in config.yaml, provide the input genome path, and then run the following command:

python run_roadies.py --cores <xxx>

Try out these steps, and let us know if you face any issues.