This repository contains the project structure, helper scripts, and sample configuration files needed to setup and run instances of T3/Breedbase for each of T3's supported crops (wheat, oat, and barley). T3's public instances can be found at the following locations:
- T3/Wheat - https://wheat.triticeaetoolbox.org
- T3/Oat - https://oat.triticeaetoolbox.org
- T3/Barley - https://barley.triticeaetoolbox.org
The hardware requirements will vary depending on the number of instances running, the number of potential concurrent users, as well as the amount and size of the data stored in the database. It is recommended to have at least 8 CPU cores and 8 GB of RAM - more will likely be needed for larger databases.
T3/Breedbase is distributed using two Docker images: one for the postgres database and another for the website. In order to install T3/Breedbase you will need to already have Docker and Docker Compose installed.
To start, first clone this repository into a directory where you will want to have all of the T3/Breedbase-related files stored (directories in this repository will be used to store the postgres data, uploaded files, etc).
git clone https://github.com/TriticeaeToolbox/breedbase.git /path/to/breedbase
By default, the docker-compose.yml file contains services that will create a separate T3/Breedbase instance
for each of the three supported crops. If you're not interested in running an instance for all of the crops, you
can remove (or comment out) the services you will not be using. This will speed up the setup process if all three
instances don't need to be created.
If you are using Docker Desktop for macOS, you may first need to give Docker permission to access the directories
on the macOS filesystem that are used as the mount points for the Docker containers. To do this, open Docker Desktop
and select Preferences => Resources => File Sharing. Here you can select the /path/to/breedbase where you cloned
the T3/Breedbase project repository.
Once you have the project repository cloned, you can use the breedbase helper script to run the intial setup script. This
script has a setup command which will download the T3/Breedbase Docker images (it will take a while to download the T3/Breedbase Web image),
setup the intial databases for each crop, and allow you to set the database and website passwords. After the initial setup finishes,
the script will automatically run the update scripts to apply any new database patches and to load the trait ontologies for
each crop.
cd /path/to/breedbase
./bin/breedbase setup
NOTE: Depending on your Docker setup, you may need to run the breedbase setup command as root or with sudo in order to
properly communicate with the Docker Daemon.
Updating T3/Breedbase requires getting new Docker images when they're made available. It is also required to run database
patches that modify the structure of your database when necessary to allow for new features. The breedbase helper script
includes an update command that will update the T3/Breedbase Docker images, run database patches, and update the trait
ontologies.
cd /path/to/breedbase
./bin/breedbase update
The breedbase helper script can be used to start and stop all of the T3/Breedbase Docker services. There is a database service
that runs a postgres server that contains a database for each of the three crops and a web service for the breedbase website
instance for each crop.
To start and stop all of the services:
breedbase start
breedbase stop
To start the website for a single crop, specify the name of the service:
breedbase start triticum # starts database (if not already running) and web service
breedbase stop triticum # stops the web service
To get the status of which services are running:
breedbase status
To view the breedbase error log for a web service:
breedbase log triticum
Once the service is running, the website will be available on the exposed port for each service:
- triticum: 8080
- avena: 8081
- hordeum: 8082
To view the website in your browser, navigate to http://localhost:{port}
For production systems, it is recommended that you put the T3/Breedbase web services behind a proxy server, such as NGINX, and forward the traffic to the appropriate port.