T3/Breedbase Docker Image

This repo contains the Dockerfile for building the T3 version of breedbase. This repository is a fork of the the original Breedbase Dockerfile. T3 will periodically update this image and it is available for download on Docker Hub as triticeaetoolbox/breedbase_web.

If you are looking run a prebuilt T3/Breedbase image, follow the instructions in the TriticeaeToolbox/breedbase repository. This repo includes instructions on how to set up your Docker host along with helper scripts to setup the intial Breedbase instance(s) and update them when a new image is released.

The main differences between this T3 version of Breedbase and the original Breedbase image include:

• the use of the T3 sgn repo (main codebase for breedbase)
  • the T3 version includes some T3-specific changes and features
• pre-loaded trait ontologies for wheat, oat, and barley
• can be used in conjunction with the TriticeaeToolbox/breedbase repository for the Docker host setup and helper scripts

Build Instructions

Update Repositories

Before building the new Docker image, make sure the t3/master branch of the TriticeaeToolbox/sgn repo and all of the instance branches (triticum, triticum-sandbox, avena, etc) of the TriticeaeToolbox/mason repo are updated with the latest changes that are to be included in the new Docker image build.

For example, to update the t3/master branch of the TriticeaeToolbox/sgn repo with changes from the upstream solgenomics/sgn repo using a specific tag:

djw64:sgn ● t3/master:✓ $ git remote -v
origin  [email protected]:TriticeaeToolbox/sgn.git (fetch)
origin  [email protected]:TriticeaeToolbox/sgn.git (push)
sgn     [email protected]:solgenomics/sgn.git (fetch)
sgn     [email protected]:solgenomics/sgn.git (push)
djw64:sgn ● t3/master:✓ $ git fetch origin
djw64:sgn ● t3/master:✓ $ git checkout t3/master
djw64:sgn ● t3/master:✓ $ git pull
djw64:sgn ● t3/master:✓ $ git fetch sgn
djw64:sgn ● t3/master:✓ $ git merge sgn-309.0
# Fix file conflicts and commit the changes here, if necessary
# Test the code for any major issues
djw64:sgn ● t3/master:✓ $ git push
# !! Remember to push the tags as well, if you want the latest 
# tag to be displayed in the footer of the website
djw64:sgn ● t3/master:✓ $ git push --tags

Build Docker Image

On TCAP, the build repository is located at /opt/breedbase-dev/breedbase_dockerfile/

To build the image using Docker, use the ./scripts/build.sh script:

./scripts/build.sh --update

This script will:

• initialize the submodules
• if the --update flag is provided:
  • pull in the most recent commits to all of the submodules
  • if this flag is not provided, the submodules will be locked to the commits that were used the last time this repo was updated
• build the T3/Breedbase Docker image
• tag the newly built image with the latest and YYYYMMDD tags

Deploy Docker Image

To deploy the image to Docker Hub, first make sure you are logged in using your Docker account (docker login).

Then, run the deploy script to push the image to docker hub using the YYYYMMDD and latest tags.

./scripts/deploy.sh

Update Instances

Once the images have been deployed to Docker Hub, use the breedbase script to pull the new images and run the update scripts (run database patches, update trait ontologies, etc) on each server (TCAP, TCAPG, and TCAPS).

breedbase update