A web application for exploration of biological data

The following tools need to be installed separately (e.g., with Homebrew) before Iris and its dependencies can be installed:

• node (nodejs.org)
• git (git-scm.com)
• gcc
• mongodb (mongodb.org)

Iris is equipped with a command-line tool, quaintly named iris, to manage the project. It can be used to install dependencies, start Iris and it services, monitor Iris, and shut it down.

To use the tool, run:

source iris.env

To install Iris, along with its dependencies, run:

iris install

To check the installation, and execute project tests, run:

iris check

To install example data used by the demo, run:

iris examples

Iris services are configured in a simple configuration file in conf/services.json listing an HTTP port, the name of the service, the Node.js control file, and a configuration file. A sample services configuration is available at conf/services-sample.json. To get started:

cp conf/services-sample.json conf/services.json

To start Iris, run:

iris start

All the services configured in conf/services.json are started. Their process IDs and network ports are listed.

To stop Iris, run:

iris stop

To restart Iris, run:

iris restart

To determine whether Iris and its services are running, run:

iris status

Each of the above management commands can be run on individual services by supplying the service name as an argument:

iris {start,stop,restart,status} <service-name>

The iris tool has a general and command-specific help facility. To find out more about it, run:

iris help [<command>]

The Iris server is run out of /nodejs. /nodejs also contains the Express routes (app.js and routes/) and Jade templates (views/).

Client-side rendering code (HTML, CSS, Javascript) is organized under /root. All client-side Javascript is in /root/js. The widgets/ directory contains the widget code, while all utility, administrative, and external scripts (jquery.js, bootstrap) should be placed at the Javascript root.

The Fastbit source code, including pristine and Iris-specific is under the /fastbit directory, but compiled artifacts are placed in folders at the root directory (/bin, /lib, /share, /include).

All the conventions above are so far tentative and up for discussion.

Copyright (c) 2012 Ware Lab, Cold Spring Harbor Laboratory