epinano_support

The dockerfile creates a docker that runs EpiNano. It is a revised version of the Dockerfile in the EpiNano repository.

After building the docker, it is run interactively. e.g.

docker run -it --rm \
-v /mnt/:/mnt/ \
--entrypoint=/bin/bash \
hbeale/tree_epinano:1

and EpiNano is called with a command like

python3 /usr/local/bin/EpiNano/Epinano_Variants.py -R $ref_fa -b $bam -n 6 -T t -s /usr/local/bin/EpiNano/misc/sam2tsv.jar