Editing a Dockerfile so the image is not run in an interactive shell, but from the ENTRYPOINT - docker

Question

I'm trying to use the docker image of a specific software (picard), and that image is designed to be run interactively, in fact, an already built docker image is provided via Dockerhub:
docker pull broadinstitute/picard
This image works perfectly will the following command:
sudo docker run -i -t -v $PWD:/usr/working broadinstitute/picard
So that within the image one could launch the actual program like:
java -jar /usr/picard/picard.jar [COMMAND] [OPTIONS] ...
What I am trying to accomplish is to execute this image without entering in an interactive shell, simply as:
sudo docker run --rm -v $PWD:/usr/working broadinstitute/picard [COMMAND] [OPTIONS] ...
As far as I understand, this could be done by creating an ENTRYPOINT in the Dockerfile (see it in appendix below), but addind the following line at the bottom of the Dockerfile will not work:
ENTRYPOINT ["java -jar /usr/picard/picard.jar"]
Instead, when I run the image as above, no output is generated, and if a specific command is called (e.g. CreateSequenceDictionary), I get the following error:
docker: Error response from daemon: OCI runtime create failed: container_linux.go:345: starting container process caused "exec: \"CreateSequenceDictionary\": executable file not found in $PATH": unknown.
What am I missing?
Dockerfile
The dockerfile can be found in the github repo at: https://github.com/broadinstitute/picard/blob/master/Dockerfile. It looks like the following:
FROM openjdk:8
MAINTAINER Broad Institute DSDE <dsde-engineering#broadinstitute.org>
ARG build_command=shadowJar
ARG jar_name=picard.jar
# Install ant, git for building
RUN apt-get update && \
apt-get --no-install-recommends install -y --force-yes \
git \
r-base \
ant && \
apt-get clean autoclean && \
apt-get autoremove -y
# Assumes Dockerfile lives in root of the git repo. Pull source files into container
COPY / /usr/picard/
WORKDIR /usr/picard
# Build the distribution jar, clean up everything else
RUN ./gradlew ${build_command} && \
mv build/libs/${jar_name} picard.jar && \
./gradlew clean && \
rm -rf src && \
rm -rf gradle && \
rm -rf .git && \
rm gradlew && \
rm build.gradle
RUN mkdir /usr/working
WORKDIR /usr/working

Answer 1

The problem is how the ENTRYPOINT is defined.
It should be
ENTRYPOINT ["java", "-jar", "/usr/picard/picard.jar"]
src: https://docs.docker.com/v17.09/engine/reference/builder/#entrypoint

Answer 2

I just learnt about other possible alternative that does not require to modify the original dockerfile, which is overriding the default ENTRYPOINT from the CLI (even if the original image does not define one).
This can be done with the --entrypoint option, but it will only take the name of the file to be executed within the image. If additional arguments are to be used, these must be called after the image name. For example:
docker run --entrypoint="java" $PWD:/usr/working broadinstitute/picard -jar /usr/picard/picard.jar [COMMAND] [OPTIONS]
This blog explains a bit more on the topic.