Discover aidenlab/Juicebox Open Source project

Breaking News!

This codebase is in the process of being split up to better support long-term maintenance and modular aspects of different tools available. The new repositories will be:

JuiceboxGUI for visualization of Hi-C maps with Juicebox Desktop and genome assembly correction with Assembly Tools.
HiCTools for building and writing .hic files (Pre, Addnorm, and Statistics)
JuicerTools for downstream analysis of .hic files (HiCCUPS, Arrowhead, APA, etc.)
Java Straw to quickly read and stream data from .hic files into Java, and is used by the above repositories.

We also have new tools:

Straw to quickly read and stream data from .hic files into C++, python, R, and MATLAB.
POSSUMM for new C++ code to rapidly calculate A-B compartments (i.e. eigenvectors) for higher resolutions
EMT for upgrading older .hic files or making smaller .hic files for regions of interest.

About Juicebox

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools . Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden. Past contributors include Ido Machol, Zulkifl Gire, Marie Hoeger, Fanny Huang, Nam Hee Kim, Vi Nguyen, Jay Ryu, Nathaniel T. Musial, and Ragib Mostofa.

Ongoing development work is carried out by Muhammad Saad Shamim, Neva C. Durand, and Olga Dudchenko.

Questions?

For FAQs, or for asking new questions, please see our forum: aidenlab.org/forum.html.

IntelliJ Setup

Use IntelliJ IDEA (Community edition - free)

To set up in IDEA, have the Java SDK installed then you'll point to it (IntelliJ has lots of documentation on this sort of thing).

Then go to VCS -> checkout from version control.
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 CLT.

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="https://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.

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 https://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please go to https://www.java.com/download.

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

To launch the Juicebox application from command line, type java -Xms512m -Xmx2048m -jar Juicebox.jar

Note: 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.

Documentation

We have extensive documentation for how to use Juicebox at https://github.com/theaidenlab/juicebox/wiki including a video, a Quick Start Guide, and a detailed tutorial.

For using Juicebox to assemble genomes see https://www.aidenlab.org/assembly/.

Command Line Tools Usage

See the documentation at https://github.com/theaidenlab/juicer/wiki for information on how to use the Juicer tools.

Compiling Jars from Source Files

You should have Java 1.8 JDK and Apache Ant installed on your system. See below for more information.
Go to the folder containing the Juicebox source files and edit the juicebox.properties file with the proper Java JDK Address.
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.
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: https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html (Alternative) For Ubuntu/LinuxMint https://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 (https://brew.sh/) on your machine See the following Stackoverflow post for more details: https://stackoverflow.com/questions/3222804/how-can-i-install-apache-ant-on-mac-os-x

Windows Installing Ant requires some minor changes to your system environment. Follow the instructions in this article: https://www.nczonline.net/blog/2012/04/12/how-to-install-apache-ant-on-windows/

Linux In the command prompt, type sudo apt-get install ant or sudo yum install ant depending on your package installer

aidenlab/Juicebox

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