Juicer: Difference between revisions

Latest revision as of 17:20, 24 March 2025

Description

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. The juicer pipeline submits jobs to the cluster and then exits. It can therefore be run on the login node. Individual tools (see $HPC_JUICER_DIR/scripts) can be run as batch jobs or interactively. Type "juicer.sh -h" to see options and help menu.

Juicer depends on reference files (bwa index plus chromosome sizes file) and restriction enzyme files that are part of the central install. You can build additional references yourself or ask UFRC staff to generate them centrally. See $HPC_JUICER_DIR/references and $HPC_JUICER_DIR/restriction_sites for available reference data.

Environment Modules

Run module spider juicer to find out what environment modules are available for this application.

System Variables

HPC_JUICER_DIR - installation directory
HPC_JUICER_BIN - executable directory

Additional Information

The juicer pipeline creates a series of batch jobs and submits them all at once using job dependencies. The main script has to be run on the login node.

We provide four variants of the main script with different resource options:

juicer.sh -- submit all jobs to investment qos of user's default (primary) account.
juicer-b.sh -- same as juicer.sh; additionally submit alignment jobs to the burst qos of user's primary account.
juicer_2ndgrp.sh -- submit all jobs to an account specified with the -A option. Facilitates use of secondary account resources.
juicer_2ndgrp-b.sh -- same as juicer_2ndgrp.sh; additionally submit alignment jobs to the burst qos of specified account.

Type "juicer.sh -h" to see options and help menu.

Template script - change "group" to user's primary or secondary group:

$ juicer_2ndgrp-b.sh \
-d /blue/group/$USER/juicer \
-A "group" \
-C 40000000 \
-z $HPC_JUICER_REFS/hg38.fa \
-y $HPC_JUICER_SITES/hg38_Arima.txt \
-p $HPC_JUICER_SITES/hg38.chrom.sizes \
-t 4

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Genomics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|juicer}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 35: / Line 35: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+The juicer pipeline creates a series of batch jobs and submits them all at once using job dependencies. The main script has to be run on the login node.
+We provide four variants of the main script with different resource options:
+* juicer.sh -- submit all jobs to investment qos of user's default (primary) account.
+* juicer-b.sh -- same as juicer.sh; additionally submit alignment jobs to the burst qos of user's primary account.
+* juicer_2ndgrp.sh -- submit all jobs to an account specified with the -A option. Facilitates use of secondary account resources.
+* juicer_2ndgrp-b.sh -- same as juicer_2ndgrp.sh; additionally submit alignment jobs to the burst qos of specified account.
+Type "juicer.sh -h" to see options and help menu.
+Template script - change "group" to user's primary or secondary group:
+ $ juicer_2ndgrp-b.sh \
+ -d /blue/group/$USER/juicer \
+ -A "group" \
+ -C 40000000 \
+ -z $HPC_JUICER_REFS/hg38.fa \
+ -y $HPC_JUICER_SITES/hg38_Arima.txt \
+ -p $HPC_JUICER_SITES/hg38.chrom.sizes \
+ -t 4
 |}}