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google-deepmind / alphafold3

AlphaFold 3 inference pipeline.
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Cannot download to /srv, despite having permissions to. #17

Closed emwjacobson closed 1 week ago

emwjacobson commented 1 week ago

Hello,

When attempting to download to a subdirectory of /srv, I would get an error saying that it needs to be run as root or have permissions for /srv, despite having appropriate permissions to write in the subdirectory.

https://github.com/google-deepmind/alphafold3/blob/0341fb7f244779a634702d7cb6e37e540e2db26a/fetch_databases.py#L94-L97

Removing the check resolves the issue and allowed me to download, just thought I would mention it :)

Augustin-Zidek commented 1 week ago

Yes, you are right, the check is too strong. All that we need to check is this:

if not os.access(args.download_destination, os.W_OK):
  raise ValueError(f'You do not have permissions to write to {args.download_destination}.')

We will send a fix, but the workaround -- as you say -- is to simply remove the check.

Thanks for reporting!

Augustin-Zidek commented 1 week ago

Fixed in https://github.com/google-deepmind/alphafold3/commit/44e1fd572a6da02c81e2b3aed94dc9b0d564375c.