Containers

TRIBES docker image includes the pipeline and all the dependences and it’s publicly available from https://hub.docker.com/r/piotrszul/tribes as docker.io/piotrszul/tribes and the most recent version can pulled with:

docker pull docker.io/piotrszul/tribes

To use a specifc version e.g.: 0.2.0 please use docker.io/piotrszul/tribes:0.2.0 as the docker image name.

It’s an executable image with snakemake as an entry point.

When running using docker it’s necessary to mount the reference data and pipeline data volumes (or local filesystem) so that the container have access to both, e.g:

docker run -it --rm -v <path-to-ref-data>:<path-to-ref-data> -v <path-to-data>:<path-to-data> docker.io/piotrszul/tribes -d <path-to-data> <other_options> ...

When running with singularity this may not be need if the volumes with data and reference data are mounted as per configuration. One important consideration though is to use -e flag as some host environment variables (e.g. related to pyton) casue issues while running in the containter:

singularity run -e  docker://docker.io/piotrszul/tribes -d <path-to-data> <other_options> ...