problem with - v

[Ferxengutta]

Hello Dear Christoph

Iḿ working wit the Docker images of MITObim, I can made all tutorials with any problem, but now I want to make a conection between my Documents and the repository, I tried using the command
sudo docker run -v PATH/to/my/Data:/name_of_the_folder_in_docker_MITObim, but doesn't create the volume, Do I need some special permission to make the conection work?

Best regards

[chrishah]

Hi,

Sorry - just saw this now. No, normally you don't need any special permissions. Not sure what the problem is - perhaps I can help if you let me know how exactly you call the docker image.

Depends on what you want to do - 2 options:

1. run the docker container like an executable - you can specify the working directory in the container via the -w option. In this case the working directory in the container does not really matter - it just exists while the container is running as the place where it is connected to the local machine. If it does not yet exist in the container it will just be created. The --rm just removes the container after it's done.
   docker run --rm -v $(pwd):/in -w /in chrishah/mitobim MITObim.pl the rest of your command

2. Enter the container and run MITObim within it. In this case I'd recommend you use an existing directory as the mountpoint within the container, e.g. /home/, which is also preset as the working directory in the docker image during build.
   docker run --rm -v $(pwd):/home -w /home chrishah/mitobim /bin/bash

The data you want to access with the container needs to be below your mountpoint on your local machine. I use $(pwd) as present working directory. From there you can then specify the location of your files via relative paths.

Perhaps this helps - let me know how it is going.

cheers,
Christoph