Holland Computing Center
HCC-DOCS
Introduction to HPC
Creating an Account
Setting Up and Using Duo
Changing Your Password
Connecting to HCC Clusters
Connecting with Terminal
Connecting with PuTTY (Windows)
Connecting with MobaXterm
Basic Linux commands
How to setup X11 forwarding
Reusing SSH connections
Handling Data
Data Storage
Using Scratch
Linux File Permissions
Using Attic
Using the /common File System
Preventing File Loss
Integrating Box with HCC
The Nebraska Research Data Storage (NRDStor)
MacOS
Smbclient
Swan
Windows
Using NU's Gitlab instance
Setting up GitLab on HCC Clusters
Data Transfer
Globus Connect
Activating HCC Cluster Collections
File Transfers Between Collections
File Transfers to and from Personal Workstations
File Sharing
Creating Globus Groups
Globus Command Line Interface
Activating UNL OneDrive on Globus
File Transfer with scp
File Transfer with WinSCP
File Transfer with CyberDuck
High Speed Data Transfers
Using Rclone for File Transfer
Connecting to CB3 iRODS
Sharing data on Swan
Running Applications
Using Preinstalled Software
Available Software for Swan
Using Custom Software
Using Anaconda Package Manager
Compiling an OpenMP Application
Using Apptainer and Docker Containers
Installing Perl modules
Using R Libraries
Application Specific Guides
Fortran/C on HCC
Bioinformatics Tools
Alignment Tools
BLAT
Bowtie
Bowtie2
Clustal Omega
TopHat/TopHat2
BLAST
Running BLAST Alignment
Create Local BLAST Database
BWA
Running BWA Commands
Biodata Module
Data Manipulation Tools
SRAtoolkit
BamTools
Running BamTools Commands
SAMtools
Running SAMtools Commands
De Novo Assembly Tools
Oases
Ray
SOAPdenovo2
Trinity
Running Trinity in Multiple Steps
Velvet
Running Velvet with Paired-End Data
Running Velvet with Single-End Data
Running Velvet with Single-End and Paired-End Data
Pre-processing Tools
Cutadapt
PRINSEQ
Scythe
Sickle
TagCleaner
QIIME
Reference-Based Assembly Tools
Cufflinks
Tools for Removing/Detecting Redundant Sequences
CAP3
CD-HIT
MPI Jobs on HCC
Allinea Profiling & Debugging Tools
Allinea Performance Reports
BLAST with Allinea Performance Reports
LAMMPS with Allinea Performance Reports
Ray with Allinea Performance Reports
Using Allinea Forge via Reverse Connect
Building LIS
Building WRF
DMTCP Checkpointing
Install and Running Matlab CobraToolbox, Gurobi, and IBM ILOG CPLEX
Running Gaussian at HCC
Running OLAM at HCC
Running Paraview
Running PostgreSQL
Running SAS on HCC
Running Theano
Visual Studio Code on HCC resources
Running JupyterLab Notebooks with Slurm
Submitting Jobs
Creating an Interactive Job
Submitting a Job Array
Submitting GPU Jobs
Submitting an MPI Job
Submitting an OpenMP Job
Job Dependencies
Monitoring Jobs
GPU Monitoring and Optimizing
Available Partitions
Available Partitions for Swan
HCC Acknowledgment Credit
Application Specific Guides
Applications Examples
Abaqus 2019 Example
Abaqus 6.14.2 Example
Comsol Example
Gamess Example
Gaussan-09 Example
Gaussan-16 Example
R Example
R-Advanced Example
fluent-19.2 Example
gromacs Example
jupyter Example
ls-dyna Example
mathematica Example
matlab Example
postgresql Example
python Example
sas Example
turbowave Example
Submitting ANSYS Jobs
Submitting MATLAB Jobs
Submitting R Jobs
HCC OnDemand
Connecting to HCC OnDemand
Managing and Transferring Files with HCC OnDemand
Job Management and Submission with HCC OnDemand
Shell Access with HCC OnDemand
Virtual Desktop and Interactive Apps with HCC OnDemand
CryoSPARC Interactive App
Anvil: HCC's Cloud
Adding SSH Key Pairs
Anvil Instance Types
Available images
Connecting to Linux Instances from Mac
Connecting to Linux Instances from Windows
Connecting to Linux Instances using X2Go
Connecting to Windows Instances
Connecting to the Anvil VPN
Creating SSH key pairs on Mac
Creating an Instance
Creating and attaching a volume
Formatting and mounting a volume in Linux
Formatting and mounting a volume in Windows
Resizing an instance
Using MySQL instances
What are the per-group resources limit?
The National Research Platform
Quick Start
Basic Kubernetes
GPU Pods
Batch Jobs
Deployments
Storage
JupyterHub Service
The OSG Consortium
Characteristics of an OSG friendly job
FAQ
Common Retirement
HCC Class Info for Instructors
HCC Class Info for Students
I have an HCC account, now what?
SSH host keys
Good HCC Practices
ATTIC Guidelines and Best Practices
Contact Us
hcc.unl.edu
Clear History
Improve this page
HCC Documentation
>
Running Applications
>
Application Specific Guides
>
Bioinformatics Tools
> Reference-Based Assembly Tools
Reference-Based Assembly Tools
Cufflinks
QIIME
Cufflinks