I cannot retrieve my pdb file- using powershell as Admin about arpeggio HOT 3 CLOSED

Hi Harry,
I was able to adapt the code for Windows using :
docker --rm -v c:/:/ -it arpeggio python arpeggio.py / [options] -v
I'm sharing it here if anyone ends up having the same issue.
c:/:/ used as :<container_path>
Thanks for the help.
Kind regards,
Maria

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Just an update,
I'm running this on User now to avoid killing Windows, this is what's coming up now:
PS C:\Users\Usuario> docker run --rm -v :/run -it harryjubb/arpeggio python arpeggio.py Cb2HU210_fixed6.pdb -v
INFO//14:39:35.851//Program begin.
Traceback (most recent call last):
File "arpeggio.py", line 708, in
s = pdb_parser.get_structure('structure', pdb_filename)
File "/usr/local/lib/python2.7/site-packages/Bio/PDB/PDBParser.py", line 85, in get_structure
with as_handle(file, mode='rU') as handle:
File "/usr/local/lib/python2.7/contextlib.py", line 17, in enter
return self.gen.next()
File "/usr/local/lib/python2.7/site-packages/Bio/File.py", line 113, in as_handle
with open(handleish, mode, **kwargs) as fp:
IOError: [Errno 2] No such file or directory: 'Cb2HU210_fixed6.pdb'

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Hi Maria,

I'm not able to test on Windows, but it may be a problem with the arguments passed to Docker, specifically the bind mount, -v :/run.

The left hand side of the : needs to have the folder containing your PDB file, this is then mapped to /run in the Docker container.

In the README example, -v "$(pwd)":/run is used, where $(pwd) expands to the current working directory in Unix/Linux shells. I'm not familiar enough with Powershell to advise on the equivalent. Since it's blank, I'd assume nothing is mounted into /run in the container, which would explain why Arpeggio can't find your PDB file, and in the latter example in your first message, Docker fails at the "$(pwd)".

Let me know if changing that works. The same will apply to

-u `id -u`:`id -g`

the backticks are shell-specific interpolation, I would advise looking into the Windows equivalent of mapping user ID and group if you find that output files are only readable via administrator access.

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