![]() 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 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 >= 1.7) on Windows, Linux, and Mac OSX. 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 further difficulties using Juicer, please do not Juicer is currently in its beta release, Juicer version 1.5. 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.
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