From bb2287b0ddcf64de7905adeba54936b004f19f4f Mon Sep 17 00:00:00 2001 From: nchernia Date: Wed, 1 Feb 2023 11:18:12 -0500 Subject: [PATCH] Update README Add more links to ENCODE, make clear certain systems are no longer under active maintenance / development. --- README.md | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a1721d4..c7af159 100755 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ To access Juicer 1.6 (last stable release), please see [the Github Release](https://github.com/aidenlab/juicer/releases/tag/1.6). If you clone the Juicer repo directly from Github, it will clone Juicer 2, which is under active development. If you encounter any bugs, please let us know. +ENCODE's Hi-C uniform processing pipeline based on Juicer can be found [here](https://github.com/ENCODE-DCC/hic-pipeline). + # About Juicer Juicer is a platform for analyzing kilobase resolution Hi-C data. In this @@ -32,17 +34,19 @@ Distribution ------------ In this repository, we include the scripts for running Juicer on AWS, LSF, -Univa Grid Engine, SLURM, and a single CPU - -/AWS - scripts for running pipeline and postprocessing on AWS +Univa Grid Engine, SLURM, and a single CPU. -/UGER - scripts for running pipeline and postprocessing on UGER (Univa) +The SLURM and CPU scripts are the most up to date. For cloud computing, we recommend the [ENCODE uniform processing pipeline based on Juicer](https://github.com/ENCODE-DCC/hic-pipeline) /SLURM - scripts for running pipeline and postprocessing on SLURM -/LSF - scripts for running pipeline and postprocessing on LSF **BETA** +/CPU - scripts for running pipeline and postprocessing on a single CPU + +/AWS - scripts for running pipeline and postprocessing on AWS **Deprecated** -/CPU - scripts for running pipeline and postprocessing on a single CPU **BETA** +/UGER - scripts for running pipeline and postprocessing on UGER (Univa) **Deprecated** + +/LSF - scripts for running pipeline and postprocessing on LSF **Deprecated** /misc - miscellaneous helpful scripts @@ -55,7 +59,7 @@ and the post-processing command line tools. ### Cluster requirements: -Juicer requires the use of a cluster, with ideally >= 4 cores (min 1 core) +Juicer requires the use of a cluster or the cloud, with ideally >= 4 cores (min 1 core) and >= 64 GB RAM (min 16 GB RAM) Juicer currently works with the following resource management software: @@ -64,6 +68,8 @@ Juicer currently works with the following resource management software: - [SLURM](https://slurm.schedmd.com/download.html) - GridEngine (Univa, etc. any flavor) +We recommend [ENCODE's Hi-C processing pipeline, based on Juicer](https://github.com/ENCODE-DCC/hic-pipeline) to run in the cloud; the AWS scripts are out of date. + ### Juicer tools requirements The minimum software requirement to run Juicer is a working Java installation @@ -102,7 +108,7 @@ respective native libraries from [JCuda](http://www.jcuda.org/downloads/downloads.html). For best performance, use a dedicated GPU. You may also be able to obtain -access to GPU clusters through Amazon Web Services or a local research +access to GPU clusters through Amazon Web Services, Google cloud, or a local research institution. If you cannot access a GPU, you can run the [CPU version of HiCCUPS](https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS) directly using the `.hic` file and Juicer Tools.