Java applications into docker and into a cluster

I have developed a set of java applications for biological analysis. These work fine but require many dependencies and setting them up on a new server might be cumbersome. Now I already started playing around with dockerizing the applications and the basics seems to work alright.

Now I was wondering what the best approach would be for a docker image which requires an input file (most likely via a mounted file or as a wget) various system arguments and generates a single output file which will be pushed back to the data server.

I have looked into docker shipyard but it seems like that it was developed for running docker images and keep them running (like wordpress/mysql/etc) not for a command line initialisation and that a node takes over.

Or would it be better to use a linux grid engine which starts the docker on the node? It would be nicest if it all can work from docker itself.