rostlab/aquaria repository overview

⁠Aquaria

Simplifying the generation of insight from protein structures

⁠Install Via Docker

Make sure you have Docker⁠ installed. You can either:

• Build the Dockerfile in this repository via:
  • docker build -t rostlab/aquaria .
  • docker run -p 8009:8009 -d rostlab/aquaria
• Or pull the image from dockerhub via:
  • docker run -p 8009:8009 -d rostlab/aquaria

The node instance will then be running in the background. In linux you can access aquaria going to: http://localhost:8009, while if you use Os X you first need to get the ip address of the docker default instance docker-machine ip default and then you can navigate to that address, like: http://192.168.99.100:8009.
To view the log of Aquaria:

• Get the machine's ID by calling docker ps. You will get something like:

  CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS                    NAMES
2e52a0ce2418        rostlab/aquaria     "npm start"         5 seconds ago       Up 4 seconds        0.0.0.0:8009->8009/tcp   awesome_northcutt

• Get the logs by calling docker logs 2e52a0ce2418 (from the example above)

• You can change configuration parameters by passing ENV parameters when calling the docker run command. (e.g.: docker run -e DBUSER='myUser' -p 8009:8009 rostlab/aquaria)

⁠Install manually

Pre Installation

• (MacOS Only) install command line tools for Mac

  • Start XCode.
  • Go to XCode/Preferences.
  • Click the "Downloads" tab.
  • Click "Components".
  • Click "Install" on the command line tools line.

• Install npm and nodejs from http://nodejs.org/⁠:

curl -L https://npmjs.org/install.sh | sudo sh`
sudo npm cache clean -f
sudo npm install -g n	

Aquaria is using node version v0.10.33

• install browserify sudo npm install -g [email protected]

Installation

• Download the repository via git clone https://github.com/sacdallago/Aquaria.git

• Install and build dependencies Open Terminal and cd to root of Aquaria directory run:

  • npm install
  • npm run build you may edit the common/config.json file and change the port if required, or pass configuration options as environment variables (e.g.: DBUSER='myDbUser' npm start).

• Run:

  • npm start

Changing the code

• Aquaria uses requirejs to handle both server and client dependencies. After making changes to the client javascript files, run npm run browserify to compile the client files into 1 large file stored as public/javascripts/aquaria.js.