cwltool_in_container

docker-compose.yml for running cwltool in the docker container

What is this?

• Within Docker Container, Dockerfile and docker-compose.yml for using cwltool
  • When using Docker in cwltool in a container, use Host's Docker
  • This is mounting ${PWD}, /tmp, /var/run/docker.sock and /usr/bin/docker

How to use

$ git clone https://github.com/suecharo/cwltool_in_container.git
$ cd cwltool_in_container
$ docker-compose up -d --build
$ docker-compose exec cwltool bash

Our Test

• Using https://github.com/hacchy1983/CWL-workflows

$ git clone https://github.com/suecharo/cwltool_in_container.git
$ cd cwltool_in_container
$ docker-compose up -d --build
$ git clone https://github.com/hacchy1983/CWL-workflows
$ docker-compose exec cwltool bash
# cd CWL-workflows
# cwltool Workflows/test-workflow.cwl Jobs/small.ERR034597.test-workflow.yml