CONTRIBUTING.md

POTAGE is a web-based tool for visualising gene expression data in the context of the IWGSC CSS contigs.

For further information please follow any of these links:

• POTAGE Docker Hub for information on using the official Docker image.
• POTAGE GitHub code repository for web application source code.

Developer Information

We make use of Docker Hub's automated builds. This means that whenever the code in this GitHub repository, Docker Hub will initialise an automated build to create a POTAGE image. This image, will then be available from Docker Hub for others to use within a mater of minutes.

The general workflow for getting a new POTAGE image available on Docker Hub for everyone to use, is as follows:

First, clone the docker-potage repository from GitHub:

git clone --recursive https://github.com/CroBiAd/docker-potage
cd docker-potage

If required, update the submodule(s) to their latest commit(s):

git submodule update --recursive --remote
git add .
git commit -m "Updated submodules to latest revision"

Make any changes you see fit to the docker-potage repository, commit and push your changes to GitHub:

# Make some changes ...
# Then:
git add .
git commit -m "I made some changes"
git push

At this point, Docker Hub will initiate an automated build. You can see it's progress at https://hub.docker.com/r/crobiad/potage/builds/.

Testing Locally

If you want to test changes locally before pushing to the docker-potage repository and initiating an automated build, you can build and deploy a Docker image locally:

Build and tag a potage image:

docker build --tag crobiad/potage ./

Now run a container locally using this image, ensuring any previous containers called POTAGE are stopped:

docker stop POTAGE && \
docker rm POTAGE && \
docker run --detach \
  --name POTAGE  \
  --publish 80:8080 \
  --volume "potage_blastdb:/var/tomcat/persist/potage_data/global/blast_db" \
  crobiad/potage