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CCBR / CHAMPAGNE

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
https://ccbr.github.io/CHAMPAGNE/
MIT License
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Singularity SIF Cachedir #61

Closed kopardev closed 1 year ago

kopardev commented 1 year ago

https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/nextflow.config#L56

Make this same as RENEE /data/CCBR_Pipeliner/SIFS -->

https://github.com/CCBR/guis/blob/7ad6aa7c7d034c4323eeaab81eb0cc0f7f956a28/bin/setup#L8C19-L8C44

or /mnt/projects/CCBR-Pipelines/SIFs if on FRCE -->

https://github.com/CCBR/guis/blob/7ad6aa7c7d034c4323eeaab81eb0cc0f7f956a28/bin/setup#L11C19-L11C52

kopardev commented 1 year ago

I guess this needs to change https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/conf/biowulf.config#L28 for biowulf .... or is it https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/conf/biowulf.config#L33 or both??

kelly-sovacool commented 1 year ago

I'm not sure why the biowulf profile sets both the singularity.cacheDir and env.SINGULARITY_CACHEDIR. In theory the first one alone should be sufficient.

Edit: looks like env.SINGULARITY_CACHEDIR is also needed on biowulf, otherwise #25 & #73 happens.

kopardev commented 1 year ago

Set it to /data/CCBR_Pipeliner/SIFS then in biowulf.config. Create a frce.config and set cacheDir to /mnt/projects/CCBR-Pipelines/SIFs there. Basically, It would be nice to have all SIF files in one common location across all workflows.

kelly-sovacool commented 1 year ago

Does nextflow have an option/subcommand to pull containers without running any processes?

Alternatively we can parse conf/modules.config and write a subworkflow that requires them without running anything.