![]() 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 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 >= 1.8) on Windows, Linux, and Mac OSX. 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installation We recommend ENCODE's Hi-C processing pipeline, based on Juicer to run in the cloud the AWS scripts are out of date.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. Things like NAM and x-ports need to be directly in the plugin folder rather than nested somewhere.To access Juicer 1.6 (last stable release), please see the Github Release. are in their own folders directly in the plugin folder, buildings and other custom goodies are arranged into folders R, C, I, civic, and traffic. My folder is organized simply: all the dependencies, textures, etc. Wine only works with Intel Macs, but most of the PowerPC's are breathing their last anyway. I have no idea why FileJuicer does this - perhaps it has something to do with some ancient character limit in file names. For instance, I've been trying to get rid of static landmark files I never use for various plopable buildings I do use, but since Juicer mangles the file names, I don't know which file to move elsewhere without re-downloading the file set for the building. It runs the regular installer directly in tasteful Windows beige - the only problem is you have to direct the install to your SC4 Plugins rather than the fake Windows directory structure Wine sets up, but the file names remain the same and you don't end up with folders full of little graphic files that are only just part of the install program anyway.
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