This docker-compose.yml file specifies all of the infrastructure needed to run the current iteration of GMOD products.
We have attempted to include as many "bells and whistles" as possible, which means this approaches the level of "tech-demo" and away from something you might wish to deploy as-is. That said, the deployment is very easy to customise and adapt to your particular organisation's needs.
Galaxy ...
... allows you to load data in Apollo,
which in turn can be exported to Chado and Tripal.
But wait, there's more! Data in Chado is made available in JBrowse
$ docker-compose pull # Pull all images
$ docker-compose up -d apollo_db tripal_db # Launch the DBsIn a new terminal, in the same folder, run docker-compose logs -f in order to
watch what is going on.
$ docker-compose up -d tripal # Wait for tripal to come up and install Chado.
$ # It takes a few minutes. I believe you'll see an apache error when ready.
$ docker-compose up -d # This will bring up the rest of the services.
| Service | Address |
|---|---|
| Galaxy | :8200 |
| Tripal (/tripal) | :8200/tripal |
| Apollo (through Galaxy, /apollo) | :8200/apollo |
| Chado JBrowse Connector | :8200/jbrowse/ |
| PostgREST | :8200/postgrest |
| PostGraphQL GraphiQL interface | :8200/graphiql |
| PgAdmin4 | :8201/ |
| Chado PostGraphQL Connector | :8200/jbrowse_graphql/ |
| Service | Username | Password |
|---|---|---|
| Galaxy | [email protected] | admin |
| Tripal | admin | changeme |
| Apollo | [email protected] | password |
The Apollo account is only used internally by the Galaxy tools. You should be automatically logged in with your Galaxy account when connecting to Apollo (thanks to gx-cookie-proxy).
This docker-compose.yml depends on a large number of containers. We link some
build status images here for developer convenience
| Image | Status |
|---|---|
| galaxy | |
| postgrest | |
| postgraphql |  |
| chado-jb-connector | |
| chado | |
| tripal | |
| gx-cookie-proxy |
Each Docker image can be configured to fit your needs. You should consult the documentation of each image, in particular:
Galaxy Docker image documentation
Tripal Docker image documentation
Chado Docker image documentation
Apollo Docker image documentation
GPLv3
This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)