![]() ![]() 4 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.3 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA Department of Computer Science, Rice University, Houston, TX 77030, USA.2 School of Medicine, University of California San Diego, La Jolla, CA 92093, USA The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.1 School of Medicine, University of California San Diego, La Jolla, CA 92093, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.Installing Ant requires some minor changes to your system environment. ![]() See the following Stackoverflow post for more details: You may need to install Homebrew ( ) on your machine If Ant is not on your Mac, install it via homebrew. You can change this by editingįor Windows/Mac/Linux, the Java 1.8 JDK can be installed from here:Īnt should be installed on most Macs. The jars are written to the directory out/.The process should take no more than a minute to build on most machines. Open the command line, navigate to the folder containing the build.xml file.Juicebox.properties file with the proper Java JDK Address. Go to the folder containing the Juicebox source files and edit the.You should have Java 1.8 JDK and Apache Ant installed on your system.including a video, a Quick Start Guide, and aįor using Juicebox to assemble genomes see. We have extensive documentation for how to use Juicebox at Values may be adjusted as appropriate for your machine. The -Xmx2048m flag sets the maximum size at 2048 megabytes (2 gigabytes). Note: the -Xms512m flag sets the minimum memory heap size at 512 megabytes, and Java -Xms512m -Xmx2048m -jar Juicebox.jar To launch the Juicebox application from command line, type We recommend having at least 2GB free RAM for the best user experience with Java Runtime Environment (JRE), please go to. System requirements for running Java can be found at Java version available, but please do not use the Java Beta Version. (version > 1.6) on Windows, Linux, and Mac OSX. The minimum software requirement to run Juicebox is a working Java installation One last note: be sure to Commit and Push when you commit files, it's hidden in the dropdown menu button in the Some tools will break if there's not enough memory and the file is too large,īut don't worry about that for development 2GB should be fine. Note that the Xmx2000m flag sets the maximum memory heap size to 2GB.ĭepending on your computer you might want more or less. button next to the text box for main class Set the main class by clicking the little. You'll create two of these, one for the GUI (call it Juicebox GUI or whatever you want, really) and one for the CLT. The former turns on all warnings, the latter gives some flexibility since some people haven't updated Java to 1.8 yet. While there, also go to Java Compiler and put this into additional command line options: -Xlint:all -target 1.7 Add ?*.sizes to the list of Resource Patterns. Set this up via IntelliJ Preferences -> Compiler. You'll need to do is be sure *.sizes is included as a file to be copied over to the class files. Then go to VCS -> checkout from version control. Then you'll point to it (IntelliJ has lots of documentation on this sort of thing). To set up in IDEA, have the Java SDK installed Use IntelliJ IDEA (Community edition - free) Durand, and Olga Dudchenko.įor FAQs, or for asking new questions, please see our forum: /forum.html. Ongoing development work is carried out by Muhammad Saad Shamim, Neva C. Past contributors include Ido Machol, Zulkifl Gire, Marie Hoeger, Fanny Huang, Nam Hee Kim, Vi Nguyen, Jay Ryu, Nathaniel T. ![]() More details on how to use Juicebox for assembly. Juicebox can now be used to visualize and interactively (re)assemble genomes.Ĭheck out the Juicebox Assembly Tools Module website for Instructions below pertain primarily to usage of command line tools and the Juicebox jar files. Detailed documentation is available on the wiki. Download Juicebox here, or use Juicebox on the web. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Juicebox is visualization software for Hi-C data. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |