Installing the 4DGBWorkflow tool

The workflow tool is a python script, and is installed using pip:

$ pip install 4dgb-workflow

This will install a python module, and the 4DGBWorkflow script. This is the command that you will use when invoking the workflow in a shell. The help for the tool shows options and subcommands:

$ 4DGBWorkflow --help
usage: 4DGBWorkflow [-h] [-n] [--docker PATH] [--build-container CONTAINER]
                    [--view-container CONTAINER] [-t TAG] [--rootless]
                    {build,view,run,update,template,version} ...

Script to run docker containers for the 4DGB Workflow

positional arguments:
  {build,view,run,update,template,version}
                        Command
    build               Build a project
    view                View/Browse a project
    run                 Run the workflow
    update              Update the Docker images for the Workflow
    template            Create a template directory with example data
    version             Get version information from Docker container

optional arguments:
  -h, --help            show this help message and exit
  -n, --dry-run         Show what docker commands would be run, but don't run them
  --docker PATH         Override the path/name of the docker client executable
  --build-container CONTAINER
                        Override the name of the container used in the build step
  --view-container CONTAINER
                        Override the name of the container used in the view (browser) step
  -t TAG, --tag TAG     Version tag for the containers to use. (Default: 'latest')
  --rootless            If you are using a rootless version of Docker (or another container
                        platform), include this flag to avoid overriding the user in the
                        container. If you don't know what that means, you can ignore this :)

When you run the tool, it will download the Docker images it needs from hub.docker.com, and keep that images up to date. Thus, the first time you run the tool, you will see the download happening in the shell. It will look something like this in the shell:

$ 4DGBWorkflow run 4DGB_Project
Unable to find image '4dgb/4DGBWorkflow-build:latest' locally
latest: Pulling from 4dgb/4DGBWorkflow-build
e756f3fdd6a3: Download complete
bf168a674899: Download complete
e604223835cc: Download complete
6d5c91c4cd86: Download complete
2cc8d8854262: Downloading [================>                             ]  64.87MB/196.7MB
2767dbfeeb87: Waiting
e5f27d860d89: Waiting
98a3e4f5f5ed: Waiting
5f15c8bc4073: Waiting
0436b31f5880: Waiting
63caf3fa19f8: Waiting
ff36ae1449c0: Waiting
5811ba7542b9: Waiting
8a76051ce885: Waiting
13d42f965c06: Waiting
...

Once the docker image is updated, the command will continue. From time to time when the command is run, this update may occur. There are command line options to control this behavior (see above).