Docker notes – Bypass entrypoint – Biochemistry Computational Research Facility (BCRF)

When activated by docker run some docker container immediately start a software within. This can be useful for the author of the image, but for others it may cause issues.

Here is one example amongst many, from a series: Bioinformatics Docker Images Project which may be difficult for some users due to the use of ENTRYPOINT within the docker file (the instructions to create a docker image):

 pegi3s/clustalomega

If take a peek at the docker file you will see that the last line says:

ENTRYPOINT ["clustalo"]

This means that when the docker image is activated the program clustalo will be started which may cause the docker container to immediately shut down if you can’t provide appropriate files.

The remedy is to provide an alternate entry point at start-up. For example:

docker run -it --rm  --entrypoint "/bin/bash"  pegi3s/clustalomega

this will start the container as an interactive terminal (-it) that will be automatically removed when the container is exiting (--rm) and provides an alternate entry point that will start a bash shell. After this command the user will be looking within the container and will be able to manually start the clustalo program.