CODEWITHSUNDEEP
bashdocker
Relyativist
Relyativist

Reputation: 56

How to set up a flag to in entrypoint of docker container

I have Dockerfile with entrypoint: 

ENTRYPOINT ["bash", "-c", "source /code/entrypoint.sh | ts '[%Y-%m-%d 
%H:%M:%S]' &>> /output/stderr.log"]

and command in entrypoint.sh:

fmriprep /input /output participant --fs-license-file 
/opt/freesurfer/license.txt --use-aroma --ignore fieldmaps --n_cpus 12 -- 
force-bbr --participant_label "${ids[@]}" -w /output

How could i set flags for command inside entrypoint for example add flag --some_flag to fmriprep command to run it with 

docker run my_image --some-flag

Upvotes: 0

Views: 6370

Answers (3)

David Maze
David Maze

Reputation: 158778

If you use the JSON-array form of ENTRYPOINT, then everything in CMD is passed as command-line arguments to the entrypoint.

I would encourage not trying to write complex scripts inline in a Dockerfile or docker-compose.yml file. Write an ordinary script, COPY it into the image, and make that script the ENTRYPOINT. It can refer to the shell variable "$@" to run its CMD.

For example, I could refactor your script into:

#!/bin/bash
# I am /entrypoint.sh
"$@" | ts '[%Y-%m-%d %H:%M:%S]' &>> /output/stderr.log

#!/bin/bash
# I am /run.sh
fmriprep /input /output participant --fs-license-file  /opt/freesurfer/license.txt --use-aroma --ignore fieldmaps --n_cpus 12 --force-bbr --participant_label "${ids[@]}" -w /output $EXTRA_OPTS

And then write a Dockerfile:

...
COPY entrypoint.sh run.sh /
ENTRYPOINT ["/entrypoint.sh"]
CMD ["/run.sh"]

And then you would get to run:

docker run my_image /run.sh --some-flag

You would also get to run ordinary debugging commands like:

docker run --rm -it my_image /bin/sh
docker run --rm my_image cat /run.sh

In this specific example I would probably rely on some external system to format and capture the log messages and not try to do it inside the container. Routing Docker container logs to logstash, for instance, is a pretty typical setup.

Upvotes: 0

Sonny
Sonny

Reputation: 3183

Pass an environment variable:

docker run -e flag=somevalue my_image

You can access flag via $flag inside your Dockerfile which you can pass to your script

Upvotes: 0

Marvin
Marvin

Reputation: 1706

You should be able to pass some environnement variable from you run command to your CMD before the "cmd" is triggered. To do such, try using the '-e' clause this way (not tested, but should work):

docker run my_image -e 'EXTRA_OPTS=--some-flag'

and in your command :

fmriprep /input /output participant --fs-license-file 
/opt/freesurfer/license.txt --use-aroma --ignore fieldmaps --n_cpus 12 -- 
force-bbr --participant_label "${ids[@]}" -w /output $EXTRA_OPTS

That's the basic idea

Upvotes: 1

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