HPC Docker Path -- can you point docker invocation at a specific script?

[lstrgar]

I'm using a nextflow workflow within a shared resource HPC center where docker is not directly accessible. Rather, docker invocation is wrapped in a script with a known location, so if a user wants they will simply replace docker with that path to that script. Sudo privileges also required.

Is it possible to invoke docker this way with nextflow? When I run the workflow out of the box I see the following error message:

Command error:
  /usr/bin/docker-current: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.26/containers/create?name=nxf-F4WjtULxyVlNBD0snlj6Aveo: dial unix /var/run/docker.sock: connect: permission denied.
  See '/usr/bin/docker-current run --help'.

So far, I've tried the following approaches --

1. In the relevant module file I added beforeScript "alias docker='/path/to/docker/script'"
2. In the docker.config file I added sudo = true
3. Both 1) and 2) together
4. In the relevant module file I added beforeScript "alias docker='sudo /path/to/docker/script'"

Looking at the generated .command.run file it's apparent that steps above are being placed in the code, but I'm still not having any success.

Any suggestions would be so appreciated!

[pditommaso]

You may be trying to create a script that invokes your docker and passthrough all arguments ie.

sudo /path/to/your/docker "$@"

[lstrgar]

You're suggesting appending "$@" to the beforeScript?

[pditommaso]

No. I'm suggesting to create a script named docker with the content above, give execution permission and put in a directory into your $PATH