JUICEBOX DAB RIG SOFTWARE
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.
JUICEBOX DAB RIG HOW TO
Module website for more details on how to use Juicebox for assembly. Juicebox can now be used to visualize and interactively (re)assemble genomes. To usage of command line tools and the Juicebox jar files. Detailed documentation isĪvailable on the wiki. This distribution includes the source code for Juicebox is visualization software for Hi-C data. POSSUMM for new C++ code to rapidly calculate A-B compartments (i.e.hic files into C++, python, R, and MATLAB. Straw to quickly read and stream data from.hic files into Java, and is used by the above repositories. Java Straw to quickly read and stream data from.hic files (HiCCUPS, Arrowhead, APA, etc.) JuicerTools for downstream analysis of.
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