Docker container is too big
Instead of using one image for IMP, we should use several small images that reflect each tools used in the pipeline. This container is there for legacy purpose and because it provide a nice development environment.
But we must keep the workflow "as is" in order to be able to run it on a cluster. Basically we need to enable a switch in the IMP command line utility (like --raw-tools for instance) that translate the command line to either raw or docker tool:
bwa index vs docker run docker-r3lab.uni.lu/bwa index
For that we need some reflextopn on how to use data docker container.