ehsueh/docker-chado

Chado database container

Docker Chado Container

Built on top of a standard postgres:9.4 container, the Chado container provides the Chado schema loaded with all 5 standard ontologies.

Launching the Container

The Chado container is very simple to start, as simple as a regular postgres container:

docker run -d --name chado erasche/chado

The Chado schema in this container will not persist across restarts, to allow for that, supply a volume with -v like so:

docker run -d --name chado -v /path/to/storage:/var/lib/postgresql/9.4/ erasche/chado

The schema and five default ontologies are installed upon launch, if no chado instance is detected.

Accessing the Container

If you haven't exposed a port with the -p/-P options, you can connect to your chado container via a linked container:

docker run -i -t --link chado:db erasche/chado bash
root@0069babbd55f:/# psql -h $DB_PORT_5432_TCP_ADDR -U postgres postgres
# Password is postgres

Schema Free Container

If you do not wish to have the schema automatically installed upon launch, simply set the environment variable INSTALL_CHADO_SCHEMA to 0:

docker run -d --name chado-tools -e INSTALL_CHADO_SCHEMA=0 erasche/chado

This will let you use all the GMOD tools without needing to wait for the chado schema to install.

Yeasty Container

If you would like some default yeast data installed for you, you can supply the environment variable INSTALL_YEAST_DATA=1. This requires that you leave INSTALL_CHADO_SCHEMA=1:

docker run -d --name chado-yeast -e INSTALL_YEAST_DATA=1 erasche/chado