• Implemented using Docker containers.
• Like a virtual machine, but runs natively.
• Therefore faster and more lightweight.
• Actually, three virtual machines linked together.
• One for the database, one for the server, one for proxy.
• genomizer-admin hides all that complexity from you.

Just do this:

$ ssh genomizer
$ URL="https://github.com/genomizer/genomizer-docker/archive/master.tar.gz"
$ wget -o genomizer-docker.tar.gz $URL
$ tar xzf genomizer-docker.tar.gz
$ cd genomizer-docker
$ ./genomizer-docker deploy

This will download the latest release from GitHub.

Binaries and documentation are now built automatically by our continuous integration system.

• Check out github.com/genomizer/genomizer-downloads.

If some required software is missing, genomizer-admin will ask you to run genomizer-admin install-prereqs.

• Installs Docker and other software for you.

Can change which port to listen on and other settings via flags:

$ ./genomizer-admin help deploy
[...]

optional arguments:
-h, --help            show this help message and exit
-p PORT, --port PORT  port to listen on (HTTPS)
--http-port HTTP_PORT port to listen on (HTTP)
--server-port SERVER_PORT port to listen on (Server)
-t TMP, --tmp TMP     path to temp directory
-d DATA, --data DATA  path to data directory
-c CERT, --cert CERT  path to the certs directory
--cpu CPU             CPU limit
--ram RAM             RAM limit

Several default configurations supported (production, dev1, dev2, ...).

Simply stop the server and copy the Data/production-data directory:

$ ./genomizer-admin stop
$ tar czf backup.tar.gz /Data/production-data
$ ./genomizer-admin start

There is also a WIP backup command that does online backup, but it needs more testing.

genomizer-admin info

• Information about how the server is configured.

$ ./genomizer-admin info
RAM Limit:   -1 (unlimited)
CPU Limit:   -1 (unlimited)
Server Port: 7000
HTTP Port:   80
HTTPS Port:  443
Temp dir:    /Data/production-data
Data dir:    /Data/tmp
PGDATA dir:  /Data/tmp/pgdata
Cert dir:    /home/designer/genomizer-docker/production/cert

genomizer-admin [stop|start|restart]

• Stop/start/restart the server.

genomizer-admin destroy

• Undo all changes, start from a clean slate.

genomizer-admin shell

• Attach a shell to a running server instance.

• Choose which container to attach with -c:

$ ./genomizer-admin shell -c postgres
[...]
$ ./genomizer-admin shell -c server
[...]
$ ./genomizer-admin shell -c nginx
[...]

genomizer-admin logs

• Show logs of a running server instance.

• Again, container can be selected with -c.

• Useful for debugging.

Just run genomizer-admin help

$ ./genomizer-admin help
[...]
subcommands:
  {install-prereqs,deploy,info,stop,start,restart,backup
  ,destroy,shell,logs,debug,help}
install-prereqs     Install software required for this script to work
deploy              Deploy the given server configuration
info                Print information about deployed server instances
stop                Stop a running server instance
start               Start a stopped server instance
restart             Restart a running server instance
backup              Backup a running server instance
destroy             Stop and remove a running server instance
shell               Attach a shell to a running server instance
logs                Show logs from a running server instance
debug               Run a debugging shell (advanced)
help                Show the help message for the given command

If you find a bug, file an issue on GitHub against the genomizer-docker repo.

A test system is running on genomizer2.

These slides are available online on genomizer.github.io.

Future work:

• Online backup.
• Update the PDF manual (which still talks about Vagrant).
• Letsencrypt integration.
  • Get rid of warnings about unsigned certificates.