* : enter description of experiment, enclosed in single quotes * is the queue for running longer jobs such as the hic file * is the queue for running alignments (default "short") aligned will be created for the final alignment splits will be created to contain the temporary split files "/Users/nchernia/Downloads/neva-muck/UGER") "hg19") alternatively, it can be defined using the -z command Run the Juicer pipeline on your cluster of choice with "juicer.sh " Building new jarsĭetails on building new jars of the juicer_tools. If you cannot access a GPU, you can run the CPU version of HiCCUPS directly using the. You may also be able to obtainĪccess to GPU clusters through Amazon Web Services or a local research
#File juicer 4.7.1 download
Other versions of CUDA can be used, but you will need to download theįor best performance, use a dedicated GPU. The native libraries included with Juicer are compiled for CUDA 7 or CUDA 7.5.
Instructions for installing the latest version of CUDA can be found on the
#File juicer 4.7.1 install
You must have an NVIDIA GPU to install CUDA. The latest version of BWA should be installed from The latest version of GNU coreutils can be downloaded from To download and install the latest Java Runtime Environment (JRE), please go Minimum system requirements for running Java can be found at Latest Java version available, but please do not use the Java Beta Version. (version >= 1.8) on Windows, Linux, and Mac OSX.
#File juicer 4.7.1 software
The minimum software requirement to run Juicer is a working Java installation Juicer currently works with the following resource management software: Juicer requires the use of a cluster, with ideally >= 4 cores (min 1 core) JuicerĬonsists of two parts: the pipeline that creates Hi-C files from raw data,Īnd the post-processing command line tools. Juicer is a pipeline optimized for parallel computation on a cluster. CPU - scripts for running pipeline and postprocessing on a single CPU BETA LSF - scripts for running pipeline and postprocessing on LSF BETA SLURM - scripts for running pipeline and postprocessing on SLURM UGER - scripts for running pipeline and postprocessing on UGER (Univa) AWS - scripts for running pipeline and postprocessing on AWS Univa Grid Engine, SLURM, and a single CPU In this repository, we include the scripts for running Juicer on AWS, LSF, Questions?įor FAQs, or for asking new questions, please see our forum: /forum.html. Please see the wiki for extensive documentation. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016. Hesitate to contact us ( you use Juicer in your research, please cite: If you have any difficulties using Juicer, please do not If you are interested in running Juicer in the cloud, you may want to check out the dockerized version The main repository on Github is now focused on the Juicer 2.0 release and is under active development. The beta release for Juicer version 1.6 can be accessed via the Github Release.
In thisĭistribution, we include the pipeline for generating Hi-C maps from fastq rawĭata files and command line tools for feature annotation on the Hi-C maps. Juicer is a platform for analyzing kilobase resolution Hi-C data. If you encounter any bugs, please let us know. If you clone the Juicer repo directly from Github, it will clone Juicer 2, which is under active development. To access Juicer 1.6 (last stable release), please see the Github Release.
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