replikation/medaka repository overview

⁠docker_files

• various tools I use as docker

Example:

• using toolname (e.g. porechop or canu etc.)
  • example for a fictive input -i and output -o is given to understand docker pathing
• ${WORKDIRPATH} could be $PWD - your current working dir
• ${WORKDIRNAME} its the location in the docker, the mountpoint
  • its important for your in- and output, but choose name freely

docker run --rm -it -v ${WORKDIRPATH}:/${WORKDIRNAME} replikation/toolname \
toolname -i /${WORKDIRNAME}/input -o /${WORKDIRNAME}/output

• some of the docker have entrypoints, like unicycler or guppy
• docker with more than one executable usually dont have entrypoints
• if you need another script (e.g. "other_script.sh") overwrite the entrypoint like this: docker run --entrypoint other_script.sh