runPrep.sh misses .simg containers

ftdc-picsl / pmacsPreps

*prep wrapper scripts for the PMACS cluster

MIT License

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runPrep.sh misses .simg containers #1

Open caugolm opened 3 months ago

caugolm commented 3 months ago

I am setting up to use runPrep.sh if possible to run aslprep-0.6.0rc1, which is saved as a .simg in containers/, but runPrep.sh doesn't currently find it. Most local singularity images are saved with ".sif" extensions, but some are ".simg". The ones saved as .simg get missed by runPrep.sh at line 41: it lists available images in the containers/ dir and greps only .sif. Similarly, line 202 defines the "image" variable using only the .sif extension

cookpa commented 3 months ago

Is there a use case for simg files? I thought sif was preferred

caugolm commented 3 months ago

Not that I’m aware of. Older versions of ASLPREP used simg in their singularity examples so that’s what I’d created previously. I’m happy to change that moving forward.