Can someone explain to me

PYTHONNOUSERSITE

? I am trying to make a container for a python package called

mifaser

. I don’t have any issues running the container directly with docker or podman:

<docker/podman> run  <http://ghcr.io/vdblab/mifaser:1.64b|ghcr.io/vdblab/mifaser:1.64b> mifaser --help

However, when running via nextflow with podman, I encounter the error:

Command error: Traceback (most recent call last):
      File "/home/mambauser/.local/bin/mifaser", line 5, in <module>
        from mifaser.__main__ import main
    ModuleNotFoundError: No module named 'mifaser'

When I try via nextflow with docker, I get

.command.sh: line 4: mifaser: command not found

If I force

PYTHONNOUSERSITE="0"

in the script body, the process runs fine with nextflow+podman! But, it still fails with

.command.sh: line 2: mifaser: command not found

via nextflow+docker. Any tips would be appreciated! Dockerfile here: https://raw.githubusercontent.com/vdblab/dockerfiles/refs/heads/main/mifaser/Dockerfile

Nextflow forces

PYTHONNOUSERSITE=1

when running jobs. This is to ensure user installs don’t override the container. If your pipeline / tool requires

PYTHONNOUSERSITE="0"

to run, that means the software isn’t fully packaged in the container !

Thanks, this is great info! I gotta start testing these containers with

PYTHONNOUSERSITE=1

. I naively thought that the anything lacking dependencies would just fail by default rather than looking in the executing env.

PYTHONNOUSERSITE

is also required/useful for e.g. singularity where it helps making sure that you don't accidentally pick up a dependency that's installed in the user directory. But that shouldn't affect whatever a tool shows up in

PATH

or not.