erasche/chado repository overview

⁠Docker Chado Container

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 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/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 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

⁠Using the Container in docker-compose.yml

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.

E.g.

image: erasche/chado:1.31-jenkins97-pg9.5

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.

⁠Changelog

• 2017-02-21
  • Re-arranged image to decrease layers.
  • Added some custom SQL required for postgraphql hacks.
• [sometime recently]
  • changed PGDATA to match the current upstream value (/var/lib/postgresql/data/) rather than the version specific directory.