Built on top of a standard postgres:9.5 container, the Chado container provides the Chado schema loaded with all 5 standard ontologies.
The Chado container is very simple to start, as simple as a regular postgres container:
docker run -d --name chado erasche/chado:latest
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.
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
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.
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