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Figure out best practice way to take in smiles from standard in #67
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Here is the exact error that occurs:
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We should try calling this from python as opposed to the command line to
see how it works.
…On Tue, Jun 29, 2021, 2:16 PM megosato ***@***.***> wrote:
Here is the exact error that occurs:
$ docker run -it --rm -v $(pwd):/data adv -r inputs/4w51-cryo.pdb -c -32.355 7.263 2.207 -b 14 14 14 -e 50 -s "CC(C)Cc1ccccc1"
ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['dock', '-r', 'inputs/4w51-cryo.pdb', '-c', '-32.355', '7.263', '2.207', '-b', '14', '14', '14', '-e', '50', '-s', 'CC(C)Cc1ccccc1']' command failed. (See above for error)
/opt/conda/envs/ADVenv/.tmp776pf1ux: line 3: syntax error: unexpected "("
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This is how they are doing it (I've linked the line throwing the error): |
@robbason it works fine if you run using a call to python from the command line python
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Just so this information is consolidated here:
docker run command is tokenized below
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Something else we can try is using the python API for conda Then we can try using that to pass a command into a conda env, which should help to get around the way they are using subprocess. I was also thinking that we could provide a template |
We have issues when using containers that have a conda env as an entry point:
We need to figure out a robust way to handle this.
List of test smiles cases:
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