eschen42 / galaxy-compose

A simple composition of Galaxy from bgruening/galaxy-stable

Compose Galaxy using bgruening/galaxy-stable

Part 0 - preliminary consideration

If you want to serve Galaxy on a port different from 8080, you will have to make adjustments maually. This snippet may help you find the files to change:

find . -path ./.git -prune -o -type f -print | xargs grep 8080

As of this writing, the changes needed are:

• The GALAXY_PORT variable in the .env file (or default.env on Windows);
• docker run command in the prep.sh file.

Part 1 - create and initialize a data-storage container

You can run

./prep.sh

which automates the following:

Create storage volume galaxy-store

docker volume create galaxy-store

Validate storage volume (optional)

docker volume inspect galaxy-store

Create storage container named galaxy-store

docker create --mount source=galaxy-store,target=/export --name galaxy-store bgruening/galaxy-stable /bin/true

Initialize the storage volume (so export files get copied to volume)

Run the fullowing till it starts the web server:

docker run --rm -ti -p 8080:80 --volumes-from galaxy-store --name galaxy_bootstrap bgruening/galaxy-stable

then use ^C to quit after export volume is initialized

Part 2 - Run the composed Galaxy

Copy default.env.example to default.env (or .env on Windows). Make sure that .env is up to date, then run:

./start.sh

This script allows you to use control-C to stop the PostgreSQL database gracefully before shutting down the containers.

If you prefer, you can start the containers in the background by running:

./srv_start.sh

Then, if you want to follow the logs, you can run:

docker-compose logs -f

(Press control-C to stop following the logs.)

To shut down the containers (and shut down PostgreSQL gracefully),

./srv_stop.sh