Built on top of a standard postgres:9.5 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
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/data/ 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 -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
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
INSTALL_YEAST_DATA=1. This requires that you leave
docker run -d --name chado-yeast -e INSTALL_YEAST_DATA=1 erasche/chado
Using the Container in
It is strongly, strongly recommended that you pin your images to a specific tag of this repository. I have intentionally and unintentionally broken the
:latest images before.
Given that I as the developer have no easy way to communicate to you as the end user that breaking changes have been made (and keeping backwards compatability is prohibitve for a 1-person team..., sorry!), it is best to pin and read the changelog before upgrading.
- Re-arranged image to decrease layers.
- Added some custom SQL required for postgraphql hacks.
- [sometime recently]
PGDATAto match the current upstream value (
/var/lib/postgresql/data/) rather than the version specific directory.