Closed mariaangelesjs closed 5 years ago
mariaangelesjs
commented
5 years ago 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
harryjubb
commented
5 years ago 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.
mariaangelesjs
commented
5 years ago Hi Harry,
I was able to adapt the code for Windows using :
docker --rm -v c:/
Hi Harry, I've been trying to open my pdb file in different ways using your example, but these are the errors that are coming up. PS C:\WINDOWS\system32> docker run --rm -v :/run -it harryjubb/arpeggio python arpeggio.py pdb -s C:\WINDOWS\system32\CB2HU210_fixed6.pdb -v INFO//10:26:26.783//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: 'pdb'
PS C:\WINDOWS\system32> docker run --rm -v :/run -it harryjubb/arpeggio python arpeggio.py -s CB2HU210_fixed6.pdb -v
usage: arpeggio.py [-h] [-s SELECTION [SELECTION ...] | -sf SELECTION_FILE]
[-wh] [-mh] [-ms MINIMISATION_STEPS]
[-mf {MMFF94,UFF,Ghemical}]
[-mm {DistanceGeometry,SteepestDescent,ConjugateGradients}]
[-co VDW_COMP] [-i INTERACTING] [-ph PH] [-sa] [-a] [-he]
[-op OUTPUT_POSTFIX] [-v]
pdb
arpeggio.py: error: too few arguments
PS C:\WINDOWS\system32> docker run --rm -v :/run -it harryjubb/arpeggio python arpeggio.py /run/CB2HU210_fixed6.pdb -s RESNAME:FMM -v
INFO//10:29:02.821//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: '/run/CB2HU210_fixed6.pdb'
PS C:\WINDOWS\system32> docker run --rm -v "$(pwd)":/run -u
id -u:id -g-it harryjubb/arpeggio python arpeggio.py /run/1XKK.pdb -s RESNAME:FMM -v C:\Program Files\Docker\Docker\Resources\bin\docker.exe: invalid reference format. See 'C:\Program Files\Docker\Docker\Resources\bin\docker.exe run --help'.Note: I've given a try again with the example at the end and the same thing is happening. Kind regards, Maria