scholtalbers/planemo-docker

Yet another planemo docker image

Planemo Docker

Yet another Docker image containing Planemo and a pre-initialized Galaxy instance.

Use

• You can start the container from a directory that contains Galaxy tools. The entrypoint of the image runs planemo serve and thus your tools will be hosted in a Galaxy instance.

  # note that you can change the source directory to another location
  docker run -it --name planemo-docker --mount type=bind,source="$(pwd)",target=/var/opt/tools -P jelle/planemo-docker:galaxy-22.01
  

• Find the port on which Galaxy is hosted:

  docker port planemo-docker
  # 9090/tcp -> 0.0.0.0:55002
  

  Alternatively if the name is not found:

  docker ps | grep planemo-docker | cut -d " " -f 1 | xargs docker port
  # 9090/tcp -> 0.0.0.0:55002
  

• Test the tool on e.g. http://localhost:55002

Planemo init

You can start a bash session in the running container and init a new tool. After tool_init the tool automatically shows up in your Galaxy tool panel.

docker exec -it planemo-docker bash
cd /var/opt/tools
planemo tool_init --id 'seqtk_seq' --name 'Convert to FASTA (seqtk)'

Planemo test

Also the other planemo commands are available, like lint and test.

docker exec -it planemo-docker bash
cd /var/opt/tools
planemo test

Build

You can combine different versions of Planemo and Galaxy when building the image. PLANEMO specifies the planemo version available on pypi. GALAXY specifies the branch to clone from https://github.com/galaxyproject/galaxy/

docker build --build-arg PLANEMO=0.74.9 --build-arg GALAXY=22.01 -t jelle/planemo-docker:0.74.9-22.01 .
# or use the dev branch
docker build --build-arg GALAXY=dev -t planemo-docker:0.74.9-dev .