Biowulf High Performance Computing at the NIH
CutRunTools2 on Biowulf

CutRunTools2 is a major update of CutRunTools, including a set of new features specially designed for CUT&RUN and CUT&Tag experiments. Both of the bulk and single-cell data can be processed, analyzed and interpreted.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --ntasks=8 --cpus-per-task=6 --mem=20G --nodes=1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load CutRunTools2
[user@cn3144 ~]$ mkdir /data/$USER/cutruntools2/
[user@cn3144 ~]$ cd /data/$USER/cutruntools/
[user@cn3144 ~]$ cp -r ${CutRunTools_TEST_DATA:-none}/* .
[user@cn3144 ~]$ python ./validate.py bulk-config.json --ignore-input-output --software
[user@cn3144 ~]$ bash run_bulkModule.sh bulk-config.json test1 &>test1_bulk.out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. cutruntools2_sc.sh). For example:


#!/bin/bash
set -e
module load CutRunTools2
cd /data/$USER/cutruntools2/
cp -r ${CutRunTools_TEST_DATA:-none}/* .
python ./validate.py sc-config.json --ignore-input-output --software
bash run_scModule.sh sc-config.json

Submit this job using the Slurm sbatch command.

sbatch --ntasks=8 --cpus-per-task=6 --mem=70G --nodes=1 cutruntools2_sc.sh