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PeerHerholz / BIDSonym

a BIDS app for pseudo-anonymization of neuroimaging data
https://peerherholz.github.io/BIDSonym/
BSD 3-Clause "New" or "Revised" License
51 stars 14 forks source link

singularity pull from docker #50

Closed dmd closed 3 years ago

dmd commented 3 years ago

Trying to do it from shub yields " While pulling shub image: error fetching image to cache: failed to get manifest for: shub://PeerHerholz/BIDSonym: the requested manifest was not found in singularity hub". Doing it from Docker works.

PeerHerholz commented 3 years ago

Hi @dmd,

thanks a lot for reporting this and providing a fix. I checked things further and the problem seems to be related to neurodocker as it skips the --copy command for Singularity recipes. Till that is resolved, it might be a good idea to remove the Singularity hub option. Could I maybe ask you to add a short notice concerning the Singularity version that is required for the approach you propose, as this only works for Singularity >= 2.5 IIRC!?

dmd commented 3 years ago

Given this functionality has been in Singularity for 3 years (and Singularity is only 4 years old), I don't think a special callout is needed. It would be pretty rare for someone to be using a 3 year old Singularity, and they'll have many other problems besides that if they are.

PeerHerholz commented 3 years ago

While all of this is certainly true, I would still like to include it as it is one sentence and informative/will hopefully be helpful for some users. Some folks still run a Singularity version lower than 2.5, not because it's their choice, but because e.g. the admins of their respective HPC won't support or update something else. They will most likely run into other problems as well, true that, and it's of course not on me or the software to fix that, but I also can't take that as an excuse to not include a short notice that aims to help them. However, I will add a short notice and explanation of how to use docker2singularity for folks that need to run Singularity <= 2.5. Thanks again for reporting this issue!