Add basic container detection for local installations

georgiesamaha / configBuilder-nf

Nextflow config builder scripts for supported HPC infrastructures.

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Add basic container detection for local installations #39

Closed jfy133 closed 9 months ago

jfy133 commented 11 months ago

Attempts auto-detection of available software environments (container engines or conda)
If none found, asks user if they want to manually select
Will write to config using 'dot' config syntax if something is selected, otherwise do not write anything
- If apptainer/singularity will also write sensisble defaults (autoMount = true)

Partly addresses #17

Does not currently include checking within a module system, need to work out how to port the current code to the new functions

jfy133 commented 11 months ago

I need to go back and document functions probably, but I tihnk the quesiton text in each function makes it quite clear

georgiesamaha commented 9 months ago

@jfy133 could you help me resolve the conflict above? From my POV looks like using this section from the infrastructure branch write_config.py will undo #38.

jfy133 commented 9 months ago

Yes, I'll look into it. It's been a while though since I've looked so it'll take a bit until I remember what I was doing :laughing:

jfy133 commented 9 months ago

I think that's it, I just need to test then I'll merge :)