Compile or Contribute

Hardware and Software Requirements

The minimum software requirement to run Juicebox is a working Java installation (version > 1.6) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not use the Java Beta Version. Minimum system requirements for running Java can be found at http://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please go to http://www.java.com/download.

We recommend having at least 2GB free RAM for the best user experience with Juicebox.

Running from the jar

To launch the Juicebox application from command line, type

java -Xms512m -Xmx2048m -jar Juicebox.jar

Note that the name of the command line tools jar might change depending on the version you downloaded and the name given in the build.xml file.

Also note that the -Xms512m flag sets the minimum memory heap size at 512 megabytes, and the -Xmx2048m flag sets the maximum size at 2048 megabytes (2 gigabytes). These values may be adjusted as appropriate for your machine.

Compiling Jars from Source Files

1. You should have Java 1.8 JDK and Apache Ant installed on your system. See below for more information.
2. Go to the folder containing the Juicebox source files and edit the juicebox.properties file with the proper Java JDK Address.
3. Open the command line, navigate to the folder containing the build.xml file and type

     ant
   

   The process should take no more than a minute to build on most machines.
4. The jars are written to the directory out/. You can change this by editing the build.xml file.

Installing Java 1.8 JDK

For Windows/Mac/Linux, the Java 1.8 JDK can be installed from here:

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

(Alternative) For Ubuntu/Linux

http://tecadmin.net/install-oracle-java-8-jdk-8-ubuntu-via-ppa/

Installing Apache Ant

Mac

Ant should be installed on most Macs. To verify installation via the command prompt, type ant -version If Ant is not on your Mac, install it via homebrew. At the command prompt, type

brew update
brew install ant

You may need to install Homebrew on your machine

See this Stackoverflow post for more details.

Windows

Installing Ant requires some minor changes to your system environment. Follow the instructions in this article.

Linux

In the command prompt, type

sudo apt-get install ant

or

sudo yum install ant

depending on your package installer

Contributing to Juicebox

We use the github repository you're browsing for source control. Please feel free to report bugs or request features using the Issues tab. If you'd like to contribute, feel free to fork our repository and send a pull request with your modifications.

Coding in IntelliJ

[https://www.jetbrains.com/idea/](IntelliJ IDEA) is our preferred visual editor for Juicebox. The Community edition is free.

To set up in IDEA, have the Java SDK installed and link it with IntelliJ (IntelliJ has lots of documentation on this and will bring it up as a popup if it's not done).

• Then go to VCS → checkout from version control. (You'll need to have forked the Juicebox repo)

• You'll need to do is be sure *.sizes is included as a file to be copied over to the class files. Set this up via IntelliJ Preferences -> Compiler. Add ?*.sizes to the list of Resource Patterns.

• While there, also go to Java Compiler and put this into additional command line options: -Xlint:all -target 1.7 The former turns on all warnings, the latter gives some flexibility since some people haven't updated Java to 1.8 yet.

• Then go to Run -> Edit Configurations.

• With the + sign, add Application.

• You'll create two of these, one for the GUI (call it Juicebox GUI or whatever you want, really) and one for the command line tools

• Set the main class by clicking the little ... button next to the text box for main class

    MainWindow.java is the main method class for the visualization/GUI portion of the software.
    HiCTools.java is the main method class for the analysis/CLT portion.
  

• For the GUI under VM Options:

        -Xmx2000m
        -Djnlp.loadMenu="http://hicfiles.tc4ga.com/juicebox.properties"
  

• For the CLT use

       -Xmx2000m
  

• Note that the Xmx2000m flag sets the maximum memory heap size to 2GB. Depending on your computer you might want more or less. Some tools will break if there's not enough memory and the file is too large, but don't worry about that for development; 2GB should be fine.

• One last note: be sure to Commit and Push when you commit files, it's hidden in the dropdown menu button in the commit window.