ILRI Research Computing

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====== Juicebox tools ======
Visualization and analysis software for Hi-C data

===== Information =====

  * Version: 1.11.08
  * Added: November, 2020
  * Link: https://github.com/aidenlab/Juicebox

===== Usage =====
See versions of juicebox which are available:
<code>$ module avail juicebox</code>

Load one version into your environment and run it:
<code>$ module load juicebox/1.11.08
$ juicebox</code>

**Note:** Juicebox is a graphical application. You must enable X11 forwarding in your SSH client when connecting to HPC in order to use it.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ wget https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.jar
$ sudo mkdir -p /export/apps/juicebox/1.11.08
$ sudo cp ~/Juicebox_1.11.08.jar /export/apps/juicebox/1.11.08</code>

I created a generic ''juicebox'' wrapper for ''Juicebox_1.11.08.jar'', as it must otherwise be run with ''java -jar ..'' and is rather user-unfriendly.

///export/apps/juicebox/1.11.08/juicebox//:

<code>#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/Juicebox_1.11.08.jar $*</code>