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Use 'early' for an early exit, before the final creation of the stats and Postprocessing feature annotation remains to be completed. Use 'postproc' when the hic files have been created and only Use 'final' when the reads have been deduped into merged_nodups but theįinal stats and hic files have not yet been created.

Use 'dedup' when the files have been merged into merged_sort but Use 'merge' when alignment has finished but the merged_sort file has not Use 'chimeric' when alignments are done but chimeric handling has not finished * : must be one of 'chimeric', 'merge', 'dedup', 'final', 'postproc', or 'early'. * : 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, Google cloud, or a local research

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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

#DOWNLOAD THE NEW VERSION FOR IOS FILE JUICER 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.

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(version >= 1.8) on Windows, Linux, and Mac OSX.

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The minimum software requirement to run Juicer is a working Java installation We recommend ENCODE's Hi-C processing pipeline, based on Juicer to run in the cloud the AWS scripts are out of date. Juicer currently works with the following resource management software: Juicer requires the use of a cluster or the cloud, 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. LSF - scripts for running pipeline and postprocessing on LSF Deprecated UGER - scripts for running pipeline and postprocessing on UGER (Univa) Deprecated AWS - scripts for running pipeline and postprocessing on AWS Deprecated CPU - scripts for running pipeline and postprocessing on a single CPU SLURM - scripts for running pipeline and postprocessing on SLURM For cloud computing, we recommend the ENCODE uniform processing pipeline based on Juicer The SLURM and CPU scripts are the most up to date. 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.ĮNCODE's Hi-C uniform processing pipeline based on Juicer can be found here. 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.

Download the new version for ios File Juicer