neurovault/neurovault_fs repository overview

⁠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

1. Fork the main repository (https://github.com/NeuroVault/NeuroVault⁠)
2. Clone your fork to your computer: git clone https://github.com/<your_username>/NeuroVault
3. 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.
4. Install docker >= 1.10 (If you are using OS X you'll also need docker-machine⁠ and VirtualBox)
5. Install docker-compose >= 1.6
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
7. 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.