if i not the root ，can this workflow run without docker

[wangjiaxuan666]

Thank you very much for sharing the software.
I don't have root permission, and I can't run docker.
If not docker image, can I run it successfully?

[hailiangmei]

Hi Jiaxuan,

Sure! If you want to run WDL pipelines on a local HPC, you can use cromwell as the execution engine. It has support to convert docker image to singularity container: https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#singularity

We use cromwell and singularity on our local Slurm HPC which works smoothly.

Cheers,
Leon

[maringa780]

Hi Leon,

I have two questions related to the original question on this thread. I hope to use this workflow on our local HPC where we don't have docker, just singularity.

1. Do I need to create singularity containers using docker images or this workflow automatically does that? If the former, do I need to edit the lines in the recommended docker images file dockerImages.yml?
2. Do I need to change or add any parameter in the code below to run this workflow in singularity?
   java -jar cromwell-77.jar run -o options.json -i inputs.json --imports RNA-seq_v5.0.0.zip RNA-seq_v5.0.0.wdl

Thanks again for your help and for sharing this workflow.

Regards,

-John

[DavyCats]

Hi John,

1. Singularity will automatically convert docker images into singularity images, so there's no need to create those yourself.
2. In order to properly run cromwell on an HPC, you'll need to give it a backend configuration informing cromwell how to submit the jobs to the scheduler. As part of this configuration you'll specify that singularity gets used instead of docker. The link provided by Leon shows how to set that up. You can then run cromwell with the following command:

java -Dconfig.file=/path/to/your/config -jar cromwell-77.jar run \
  -o options.json -i inputs.json --imports RNA-seq_v5.0.0.zip RNA-seq_v5.0.0.wdl