Using HTCF

This repository includes information about software, data organization, and common workflows on the cluster.

Getting Started

Logging on and running jobs

Configure your shell environment

VSCode Setup

git and Github

(reach out to admin for permissions)Mounting LTS locally

General Use

Managing software with Spack

Running Jupyter Notebooks on the server using VSCode

Run R scripts from the command line

How do I access GitHub Copilot?

(under construction)How do I avoid losing work when I lose my SSH connection?

Data Storage

Storing raw and processed data files

Establishing data provenance

Workflows

Nextflow HTCF config

Submit batch scripts sequentially using dependancies

Parallelization

Processing paired-end read fastq files to get unique amplicon sequence counts