runDLKcat() cannot find path to data

[PkiwiBird]

When runing runDLKcat(); there's this error:

Running DLKcat prediction, this may take many minutes, especially the first time.
docker: Error response from daemon: create ~/drive/Recon4IMD/WP2_MetNetwork/T2.5_Kinetics/data: "~/drive/Recon4IMD/WP2_MetNetwork/T2.5_Kinetics/data" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path.
See 'docker run --help'.
Error using runDLKcat
DLKcat encountered an error or it did not create any output file.

when running docker run --help gave error:
Unrecognized function or variable 'docker'.

From the terminal docker seems to be installed:

 which docker
/usr/bin/docker

[mihai-sysbio]

Hi @PkiwiBird! Could you try using the full path, starting with a /, instead of starting with the ~ alias?

[mihai-sysbio]

To give more context, ~ is your home directory, but I wouldn't be surprised if the new shell, where the Docker command is run, has not been passed this alias, so it does not understand it, as if it were a relative path ../.../drive/, which would explain the error message.

[PkiwiBird]

Thank you. I don't like full paths. Do you know how to add that path to docker? just adding to .bashrc doesn't seem to work.

[mihai-sysbio]

Modifying the environment in which Docker runs would require altering the GECKO source code.

A quicker alternative would be to convert the path from avoid the ~ would be to convert it. This SO solution would work well https://stackoverflow.com/a/75470259 I think.

[PkiwiBird]

thanks!

[edkerk]

I assume that params.path in the model adapter started with ~? We can make runDLKcat turn it into a full path before calling docker, using the code @mihai-sysbio suggested.