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Example SLURM Script (from video)
(Link to original video) fastqc.sh and multiqc.sh scripts at bottom of page (slurm script) #!/bin/bash #SBATCH --job-name=qcjob #SBATCH --output=%x_%j.out #SBATCH --error=%x_%j.err #SBATCH --account=<your_department> #SBATCH --partition=compute #SBATCH --nodes...
Data transfer onto the HPC
At some point, you will inevitably need to get data from the HPC back onto your local machine, or vice versa. There are a number of different tools that can handle this, but for most use cases either rsync or scp should suffice. Transfer using GUI application ...
Running Juicer on the HPC
Setting up your juiceDir To get started with Juicer, you will need to have a directory where your input files exist. The juiceDir should contain a folder called fastq, a folder called references, and a folder called restriction_sites. The names should be exact...
Running Juicebox
ssh with X11 enabled In order to use Juicebox on the HPC, you have to ssh with X11 enabled, which allows for GUI apps to use your local computer graphics even while the software is installed on the hpc. To do this simply execute: ssh -X <your_username>@hpc1.it...
Issues Connecting to the HPC
Connection troubleshooting If you are trying to connect to the HPC (ssh <your_username>@hpc1.its.appstate.edu) but are finding that the SSH client is hanging or getting a message that the 'login has timed out', there are a few troubleshooting steps you can go ...
Patching and Pausing Jobs
On HPC1 use squeue to determine what jobs are running on what nodes: squeue --long Tue May 27 13:16:59 2025 JOBID PARTITION NAME USER STATE TIME TIME_LIMI NODES NODELIST(REASON) 8957 compute a1748355 azeezoe PEN...
TEST DELETE
Role and Support Scope
Our Systems & Research Computing IT team ensures that the infrastructure, platforms, and services you rely on are available, functional, and performant. We focus on diagnosing and resolving system-level issues so you can focus on your research and development ...