Genomics Institute Computing Information

Welcome to the Genomic Institute Computing Information Repository! Browse the below topics for help in the area you are curious about.

GI Public Computing Environment

• How to access the public servers
• Resetting your Public UNIX Password

GI Firewalled Computing Environment (PRISM)

• Access to the Firewalled Compute Servers
• Firewalled Computing Resources Overview
• Firewalled Environment Storage Overview
• Firewalled User Account and Storage Cost
• Grafana Performance Metrics
• Visual Studio Code (vscode) Configuration Tweaks
• /private/groups Data Usage Graphs
• /private/warm-archive Data Usage Graphs
• Resetting your VPN/PRISM Password

VPN Access

• Requirement for users to get GI VPN access
• Setting Up The VPN on MacOS
• Setting Up The VPN on Windows
• Setting Up The VPN on Linux
• Multi Factor Authentication (MFA) Frequently Asked Questions
• Duo Pushes Aren't Being Sent to My Phone!

NIH dbGaP Access Requirements

• Requirements for dbGaP Access

Amazon Web Services Information

• Overview of Getting and Using an AWS IAM Account
• AWS Account List and Numbers
• AWS Shared Bucket Usage Graphs
• AWS Best Practices
• AWS S3 Lifecycle Management

JupyterHub Notebooks Spawned via Slurm

• Access the JupyterHub Slurm Server
• Create a Jupyter Virtual Environment
• Change Default File Browser Directory

Slurm at the Genomics Institute

• Overview of using Slurm
• Slurm Best Practices
• Cluster Etiquette
• Annotated Slurm Script
• Job Arrays
• GPU Resources
• Quick Reference Guide
• Convenient Slurm Commands
• Slurm Queues (Partitions) and Resource Management
• Slurm Tips for vg
• Slurm Tips for Toil
• Using Docker under Slurm
• Phoenix WDL Tutorial
• Slurm Insights Dashboard

General Docker Information

• Running a Container as a non-root User

Problems or technical support

If you have any questions or problems with the GI computing environment, please send an email to cluster-admin@soe.ucsc.edu