tbepler
Alternatives to calling micrograph names as argument list in topaz extract
Hi!
I am using topaz through cryoSPARC with topaz containerized. The container calls topaz extract in the following generic way:
singularity exec container.sif bash -c "..."
This runs into the system's maximum character limit for commands at around 500-600 micrographs in our setup, which means a lot of splitting micrographs. Without containerization we had a much more permissive limit of 6000-7000 micrographs (the max argument limit being the cap), but the current one is not really tolerable for larger datasets.
My question/request is: would it be possible to refer to micrographs in topaz extract in a way that does not need to open wildcards into long lists of arguments?
Cheers, EP
Well, having made a more thorough search here, it seems something to address this is already being proposed here:
https://github.com/tbepler/topaz/pull/192
So consider this an upvote for that!
EP
Fixed in https://github.com/tbepler/topaz/commit/134096829db98134d4e563e74d487e249112cc45
