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🐳📊📚 Galaxy + Apollo + Chado + Tripal + JBrowse + JBrowse REST API + PostGraphQL + JBrowse GraphQL Experiment all as a docker-compose.yml

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Galaxy/Apollo

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.

Screenshots

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

Running

$ docker-compose pull # Pull all images
$ docker-compose up -d apollo_db tripal_db # Launch the DBs

In 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.

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/

Credentials

Service Username Password
Galaxy admin@galaxy.org admin
Tripal admin changeme
Apollo admin@local.host 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).

Dependencies

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 Docker Automated build
chado-jb-connector
chado
tripal
gx-cookie-proxy

Configuring

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

LICENSE

GPLv3

Support

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)

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🐳📊📚 Galaxy + Apollo + Chado + Tripal + JBrowse + JBrowse REST API + PostGraphQL + JBrowse GraphQL Experiment all as a docker-compose.yml

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