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Nucleoatac on NIH HPC Systems

NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data. Functions for calling nucleosomes are included in the nucleoatac command-line function. NucleoATAC also includes other utlities for working with ATAC-seq data under the pyatac function.

Batch job on Biowulf

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

#!/bin/bash
module load nucleoata

cd /data/$USER/dir
nucleoatac command
......

Then submit the file on biowulf

biowulf> $ sbatch script.sh

For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit

Swarm of Jobs on Biowulf

Create a swarmfile (e.g. script.swarm). For example:

# this file is called script.swarm
cd dir1;nucleoatac command 1; nucleoatac command 2
cd dir2;nucleoatac command 1; nucleoatac command 2
cd dir3;nucleoatac command 1; nucleoatac command 2
[...]

Submit this job using the swarm command.

$ swarm -f script.swarm --module nucleoatac

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage

Interactive job on Biowulf

Allocate an interactive session. Sample session:

[biowulf ~]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[cn1719 ~]$ module load nucleoatac

[cn1719 ~]$ nucleoatac command
Documentation
http://nucleoatac.readthedocs.io/en/latest/