Download
If you're not using HiCCUPS, any of the below jars should work on your system. Otherwise, please download the jar corresponding to your version of CUDA
Please note that these jars are compiled from the source at the Juicebox repository
Juicer Tools requires Java: download Java here Java Version 8 or higher required for the latest versions.
Due to active development, bugs may be encountered. Please email us or create a GitHub issue for these bugs and we will fix them ASAP.
Newer jar releases are posted under Github Releases in the Juicebox repo.
Dev version of SCALEv3, multithreading APA, etc.
Int vs Long bug fix.
Several bug fixes, normalization improvements, optimizations, new functionalities.
The default number of threads has been set to 1 rather than the maximum number of available CPU threads. The --threads flag can be used to increase the desired number of threads.
Re-organization of HiCCUPS and HiCCUPSDiff to reduce memory consumption and improve runtime.
New flag added for specifying the genome ID separately from the required field (which can be a chrom.sizes file); use -y genomeID
Juicer tools jar (CUDA 8 for Unix x64)
Juicer tools jar (CUDA 8 for Unix PPC)
Juicer tools jar (CUDA 8 for Windows)
Juicer tools jar (CUDA 8 for Unix)
Juicer tools jar (CUDA 8 for Windows)
Juicer tools jar (CUDA 8 for Unix)
Juicer tools jar (CUDA 8 for Windows)
Juicer tools jar (CUDA 8 for Unix)
Note that Juicer Tools used to be named Juicebox Tools.