Is it possible to have plugins live somewhere that isn t the nf-core #nextflow-plugins

Is it possible to have plugins live somewhere that...

Arthur

08/30/2023, 11:00 AM

Is it possible to have plugins live somewhere that isn’t the home directory of the user running nextflow? We are running on an HPC that is quite locked down and if we have to pre-download plugins to each users’

$HOME/.nextflow

that could be quite onerous. We have a shared nextflow binary and I am wondering if it is possible to store plugins alongside that somehow?

👀 1

Phil Ewels

08/30/2023, 11:53 AM

Can you use

NXF_HOME

Phil Ewels

08/30/2023, 11:54 AM

But plugins are usually just a few thousand lines of code. Maximum a few kb in size I would have thought. Would that be so bad for people to download?

Phil Ewels

08/30/2023, 11:54 AM

Ah, sorry - not the file size. The fact that you need to fetch in advance. Gotcha.

Arthur

08/30/2023, 12:01 PM

Yeah it’s mainly that anyone doing this would need to individually set up their copies. Ideally I would have a single location alongside our

nextflow

binary which would have a known set of plugins and we could keep a config that tracks which versions we currently have installed.

Arthur

08/30/2023, 12:03 PM

I’m not sure if setting

NXF_HOME

would have some consequences if different users were trying to run different versions of workflows (because we can access internal gitlab but not necessarily public github so not everything is needed locally)

Marcel Ribeiro-Dantas

08/30/2023, 1:05 PM

I haven’t tested this, but I think you could have the plugins in a shared drive and provide a JSON to

NXF_PLUGINS_TEST_REPOSITORY

(read here) with the local paths for these plugins so that when Nextflow tries to install them, it’ll get them from your shared drive.

Phil Ewels

08/30/2023, 1:12 PM

@Arthur if you fancy making a feature request issue about this on the Nextflow repo that'd be nice. It would be good to have an easier solution for this.

09/01/2023, 9:50 AM

use

NXF_PLUGINS_DIR

env variable

gratitude thank you 1

Phil Ewels

09/01/2023, 10:37 AM

Damn it, I knew that there was an env var like that! shakefist

Phil Ewels

09/01/2023, 10:37 AM

I even searched the Nextflow docs for exactly that string 😅

Phil Ewels

09/01/2023, 10:38 AM

Seems like it's documented in the nextflow repo under

plugins/README.md

but not in the main Nextflow docs.

Phil Ewels

09/01/2023, 10:44 AM

Made an issue to look into consolidating these into the main docs..

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