intermine/bluegenes

Name: bluegenes

Owner: InterMine

Description: A friendly next-generation interface for Genomic data discovery powered by InterMine

Created: 2016-07-27 21:58:58.0

Updated: 2017-12-12 14:20:19.0

Pushed: 2017-12-19 14:34:12.0

Homepage: http://bluegenes.apps.intermine.org

Size: 1792

Language: Clojure

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README

BlueGenes

About

BlueGenes is designed to make searching and analysing genomic data easy. It's powered by InterMine web services, meaning that the data from nearly 30 InterMines worldwide can be accessed from the same familiar interface.

Try BlueGenes now

Feedback: Please create an issue in this repo or email info - at - intermine - dot - org

Getting Started

System Requirements

• Java 1.6+
• PostgreSQL 9.3+
• Leiningen 2.5+

Initial Setup

BlueGenes has two main components: a web application and a server that hosts it. The server requires a connection to a PostgreSQL server to persist user data. We recommend creating two databases, one for development/testing and one for production:

eatedb bluegenes-dev
eatedb bluegenes-prod

You then need to configure BlueGenes to use those databases. Copy and edit the example in config/dev/README.md and save it to config/dev/config.edn and config/prod/config.edn.

Google Analytics

If you wish to track pages hits, set up Google analytics for your domain, then add your google analytics id to your config.edn files (mentioned above) or environment variables. This is completely optional.

google-analytics "UA-12345678-9"}

Compile and Run (Production)

To compile and package BlueGenes into an executable jar, run the following command in the project folder:

in uberjar

Then, to start the application, execute the jar and pass in one of the config.edn files from above:

va -jar -Dconfig="config/prod/config.edn" target/bluegenes.jar

(When executing the jar the config.edn file can be located anywhere, including your home directory for security.)

Configuration

Adding a new mine

Open src/cljc/bluegenes/mines.cljc and copy the value of the sample-mine variable into the mines hashmap. Change the key to something unique (:yourmine) and edit the default values appropriately. Be sure to edit the {:id …} value to reflect the key you used for :yourmine

 mines {:humanmine {...}
        :yourmine  {:id :yourmine
                ...})

Changing the default mine

Open src/cljs/bluegenes/db.cljs and edit the :current-mine hashmap value to the keyword of a mine in mines.cljc (see above).

 default-db
..
mine-name :yourmine
..}

Please note that you will have to recompile the application for the changes to take effect (see below). Also, may need to clear your local storage for the :default-mine to take effect. You can do this by visiting the web application, clicking the cog on the top right, selecting Debug, and then clicking the button to delete local storage.

Developers

Prerequisites and Dependencies

You will need Leiningen 2.0 or above installed (2.4+ to use the web-repl). This handles all java/clojure dependencies. As clojure is a JVM language, this requires a JDK (1.6+) be installed; please see your friendly java vendor for details.

A node-js environment is also required, which handles the installation of the javascript dependencies using npm and Bower.

Required: The InterMine you point BlueGenes at must be running InterMine

Download dependencies.

r install

Compile css file once.

 less once

Automatically recompile css file on change.

 less auto

Start the process to reload code changes in the browser:

 figwheel dev

Start the web server:

In another terminal, run the following

 with-profile +dev run

Then visit http://localhost:5000/ (or whichever port you specific in config.edn)

Run tests:

 clean
 doo phantom test once

The above command assumes that you have phantomjs installed. However, please note that doo can be configured to run cljs.test in many other JS environments (chrome, ie, safari, opera, slimer, node, rhino, or nashorn).

Production Build

 clean
 uberjar

That should compile the clojurescript code first, and then create the standalone jar.

When you run the jar you can set the port the ring server will use by setting the environment variable PORT. If it's not set, it will run on port 5000 by default.

Minified deployment using dokku

One of the easiest ways to deploy the prod minified version is to set up Dokku on your intended server. Once dokku is configured on your remote host, all you need to do to deploy a minified build is add the server as a remote and push to it:

git remote add my-awesome-server bluegenes@my-awesome-server.git
    git push my-awesome-server master

Also see the note in the next section about Postgres

Setting up bluegenes for remote deployment

Ensure that you set all [config variables](ADD LINK) and point to an existing postgres database.

In the case of Heroku, that means editing the app on the Heroku dashboard and add a Postgres service.
For Dokku, use the postgres plugin to link a postgres database.

Further help needed?

If you think the issue is related to InterMine or its webservices, check out the InterMine documentation Documentation on BlueGenes is available in the docs folder