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> ...