CODEWITHSUNDEEP
dockercontainerslocal
chainhomelow
chainhomelow

Reputation: 347

How to Run a Command in a Container Using Local Input Files without Copying

I am new to docker and containers. I have a container consisting of an MRI analysis software. Within this container are many other software the main software draws its commands from. I would like to run a single command from one of the softwares in this container using research data that is located on an external hard drive which is plugged into my local machine that is running docker.

I know there is a cp command for copying files (such as scripts) into containers and most other questions along these lines seem to recommend copying the files from your local machine into the container and then running the script (or whatever) from the container. In my case I need the container to access data from separate folders in a directory structure and copying over the entire directory is not feasible since it is quite large.

I honestly just want to know how I can run a single command inside the docker using inputs present on my local machine. I have run docker ps to get the CONTAINER_ID which is d8dbcf705ee7. Having looked into executing commands inside containers I tried the following command:

docker exec d8dbcf705ee7 /bin/bash -c "mcflirt -in /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold.nii -out sub-S06V1A_task-compound_run-01_bold_mcf_COMMAND_TEST.nii.gz -reffile /Volumes/DISS/FMRIPREP_TMP/sub-S06V1A_dof6_ver1.2.5/fmriprep_wf/single_subject_S06V1A_wf/func_preproc_task_compound_run_01_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots"

mcflirt is the command I want to run inside the container. I believe the exec command would do what I hope since if I run docker exec d8dbcf705ee7 /bin/bash -c "mcflirt" I will get help output for the mcflirt command which is the expected outcome in that case. The files inside of the /Volume/... paths are the files on my local machine I would like to access. I understand that the location of the files is the problem since I cannot tab complete the paths within this command; when I run this I get the following output:

Image Exception : #22 :: ERROR: Could not open image /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Can anyone point me in the right direction?

Upvotes: 3

Views: 4022

Answers (1)

grapes
grapes

Reputation: 8646

So if I got you right, you need to execute some shell script and provide the context (like local files).

The way is straightforward.

Lets say your script and all needed files are located in /hello folder of your host PC (no matter really if they are stored together or not, just showing the technique).

/hello
  - runme.sh
  - datafile1
  - datafile1

You mount this folder into your container to make the files accessible inside. If you dont need container to modify them, better mount in readonly mode.

You launch docker like this:

docker run -it -v /hello:/hello2:ro ubuntu /hello2/runme.sh

And that's it! Your script runme.sh gets executed inside container and it has access to nearby files. Thanks to -v /hello:/hello2:ro directive. It maps host's folder /hello into container's folder /hello2 in readonly ro mode.

Note you can have same names, I've just differed them to show the difference.

Upvotes: 3

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