docker

Galaxy Docker example deployment

If you are running Docker on OSX (Mac), first see the related subheading below. Ensure docker can be run without root privileges. Change the current working directory to /deployment/docker (the path containing this read-me). Modify ./changeme.auto.tfvars with any custom values you like. You must at least set the docker_gid variable to a group id with write access to /var/run/docker.sock. Run stat /var/run/docker.sock (or stat -x /var/run/docker.sock on OSX) to show the owning group id.

Run the following to start an instance on your local computer using docker:

terraform init
./deploy.sh

Browse to http://localhost:8000/ to access the deployment.

To shut down this instance, run ./destroy.sh. This will delete the instance, all of its data, and the container images.

OSX Peculiarities

OSX does not natively support Docker, it runs Docker within a Linux virtual machine. This workaround means that support is limited to only the most basic use case. The following needs to be added to changeme.auto.tfvars:

docker_gid = 0
docker_socket_path = "/run/host-services/docker.proxy.sock"

The last modification you need to make is to allow group write access to the docker socket within containers. To do this run the following:

docker run --rm -v /run/host-services/docker.proxy.sock:/run/host-services/docker.proxy.sock alpine chmod g+w /run/host-services/docker.proxy.sock

This command must be run any time you restart your system, before you can run deploy.sh or submit analysis. See docker/for-mac#3431 for more information about the issue.

Appropriate resources must be allocated to the Docker VM or OSX will randomly kill the application and tools during an analysis. A minimum of 8GB of RAM and 16GB of swap space is required. It is recommended to provide as much swap space as possible to avoid out of memory issues.

Providers

No providers.

Modules

Name	Source	Version
admin_user	../../modules/bootstrap_admin	n/a
galaxy	../../destinations/docker	n/a

Inputs

Name	Description	Type	Default	Required
debug	Enabling will put the deployment into a mode suitable for debugging	bool	n/a	yes
docker_gid	GID with write permission to /var/run/docker.sock	number	n/a	yes
docker_socket_path	Host path to docker socket	string	"/var/run/docker.sock"	no
email	Email address to send automated emails from	string	n/a	yes
host_port	Host port to expose galaxy service	number	n/a	yes
instance	Unique deployment instance identifier	string	n/a	yes
microbedb_mount_path	Path on host to mount microbedb to share with jobs	string	"./microbedb/mount"	no
worker_replicas	Number of worker replicas	number	1	no

Outputs

Name	Description
galaxy_admin_api_key	Galaxy admin api key
galaxy_admin_password	Galaxy admin password
galaxy_admin_username	Galaxy admin username
galaxy_endpoint	Galaxy front-end endpoint
galaxy_master_api_key	Galaxy master api key

Resources

No resources.