NeuroVault.org
Easy to use web database for brain statistical maps, atlases and parcellation maps.
How to set up NeuroVault for local development?
Installing dependencies
- Fork the main repository (https://github.com/NeuroVault/NeuroVault)
- Clone your fork to your computer:
git clone https://github.com/<your_username>/NeuroVault - Warning: if you are using OS X you have to clone the repository to a subfolder in your home folder -
/Users/<your_username>/...- otherwise docker-machine will not be able to mount code directories and may fail silently. - Install docker >= 1.10 (If you are using OS X you'll also need docker-machine and VirtualBox)
- Install docker-compose >= 1.6
- If you are using OS X and homebrew steps 3 and 4 can be achieved by:
brew update && brew install docker docker-machine docker-compose - Make sure your docker daemon is running and environment variables are configured (on OS X:
docker-machine create --driver virtualbox nv && docker-machine start nv && eval "$(docker-machine env nv)")
Running the server
docker-compose up -d
The webpage will be available at 127.0.0.1 (unless you are using docker-machine - then run docker-machine ip nv to figure out which IP address you need to use; remember that your enviroment variables need to be properly configured by running eval "$(docker-machine env nv)").
Initially, some data will be available by default with username/password neurovault/neurovault and neurovault2/neurovault2.
You can also run the server in non detached mode (shows all the logs in realtime).
docker-compose up
Stopping the server
docker-compose stop
Restarting the server
After making changes to the code you need to restart the server (but just the uwsgi and celery components):
docker-compose restart nginx uwsgi worker
Reseting the server
If you would like to reset the server and clean the database:
docker-compose stop
docker-compose rm
docker-compose up
Running Django shell
docker-compose run --rm uwsgi python manage.py shell
Running tests
docker-compose run --rm uwsgi python manage.py test
Updating Docker image
If you add a dependency (e.g., a new pip install) or modify the Dockerfile in any way, you will need to rebuild the docker image:
docker build -t neurovault/neurovault .
Using pycortex
To use pycortex you will need a different image (that includes FreeSurfer). Just change "neurovault/neurovault" with "neurovault/neurovault_fs" in docker-compose.yml. This image is significantly bigger and will take longer to download.
You can also build it locally
docker build -t neurovault/neurovault_fs -f fs_docker/Dockerfile .
Pay special close attention that the command above ends with a . to indicate the present working directory, the base of the code repository.