====== Juicer ======

Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.


===== Information =====

  * Version: 1.6
  * Added: January, 2021
  * Link: https://github.com/aidenlab/juicer

===== Usage =====

See which versions of juicer are available:
<code>$ module avail juicer</code>

Load one version into your environment and run it:
<code>$ module load juicer/1.6
$ juicer.sh -h</code>

==== Example ====

Testing juicer with the included sample data:

<code>$ module load juicer/1.6
$ mkdir -p 2021-01-18-juicer/fastq
$ cd 2021-01-18-juicer/fastq
$ wget http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz
$ cd -
$ juicer.sh -d ~/2021-01-18-juicer</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>
$ cd /tmp
$ wget https://github.com/aidenlab/juicer/archive/1.6.tar.gz
$ tar xf 1.6.tar.gz
$ cd juicer-1.6
$ mkdir references; cd references
$ wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa
$ mkdir ../restriction_sites; cd ../restriction_sites
$ wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/restriction_sites/hg19_MboI.txt
$ cd ..
$ ln -s SLURM/scripts .
$ cd scripts
$ wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar
$ ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar
$ cd ..
$ sed -i -e '/sbatch_mem_alloc/d' -e '/--mem/d' scripts/juicer.sh
# edit juicer.sh for HPC hostname stuff
$ sudo mkdir -p /export/apps/juicer/1.6
$ sudo cp -r * /export/apps/juicer/1.6
</code>

**Note 1:** There are several modifications we need to do to get juicer.sh to run on our cluster. First, the addition of a check to see if it is running at ILRI versus Aiden lab, and second to remove the SBATCH memory options because we don't use those on our cluster.