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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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Alternatives to calling micrograph names as argument list in topaz extract #201

Open epkumpu opened 6 days ago

epkumpu commented 6 days ago

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

epkumpu commented 6 days ago

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