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khanlab / hippunfold

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
https://hippunfold.readthedocs.io
MIT License
46 stars 12 forks source link

Added missing container for hippdwi_to_template #216

Closed kaitj closed 2 years ago

kaitj commented 2 years ago

This PR adds the autotop container to fix the missing command error for c3d when the hippdwi_to_template rule is run.

Resolves #215

akhanf commented 2 years ago

actually wait, now having some strange issues with the version of c3d in that container - the rule runs fine with c3d installed on cbs server.. Will see if maybe upgrading to autotop 0.4.2 fixes it

akhanf commented 2 years ago

nevermind, the issue I was just having is actually a separate one, related to reading in files from home directory (or ~/graham) when using a container rule in snakemake -- it changes the home directory when running singularity, so need to have SINGULARITY_BINDPATH that includes /home/ROBARTS:/home/ROBARTS. I'm in the process of making this the default on the system, but will make sure we note this in the documentation too..

So I'll merge this in!