HMS IT RC O2

Troubleshooting Slurm Jobs

Moving from Orchestra to O2

Report CPU/Mem usage in slurm job standard output

Submitting data to GEO

Get information about current and past jobs

Published Papers That Used O2, Orchestra, or Research Computing

Text for Grants Referring to the HMS Research Cluster

Using Mathematica on O2

The O2 Open OnDemand Pilot

sratoolkit/2.10.7 to download NCBI SRA data

Using O2 GPU resources

Scratch_gpu Storage

Using Software Provided by BioGrids

O2 Resource Utilization

Using Slurm Basic

Get more informative slurm email notification

Local Software Installs

Batch small jobs together as a big job

UNIX Permissions Tutorial

Using X11 Applications Remotely

Public Databases

sratoolkit/2.10.7 to download dbGAP data

spp (1.15.2) for Chip-Seq

O2 cron service

How To Submit Parallel Jobs in O2

Personal Perl Packages

Using Aspera to Download Data

Get more informative slurm email notification and logs through rcbio/1.3.3

Understanding O2 Slurm Accounts/Associations and Unix Accounts/Groups

Using AlphaFold on O2

Frequently Asked Questions and Answers

tmux: Keep Linux Sessions Alive (so you can go back to the same terminal window from anywhere, anytime)

Scratch3 Storage

Two Factor Authentication FAQ

Filesystem Quotas

How to troubleshoot the sratoolkit/2.10.7 module

UCSC Genome Browser and IGV access for data on O2

Running Singularity Containers in O2

Using Java on O2

GATK4 Mutect2 using Singularity Container

O2 HPC Cluster and Computing Nodes Hardware

Currently Available Software on O2

How to login to O2

Personal R Packages

Installing Other R packages on O2

How to Generate SSH Keys

Using Applications on O2

GATK4 RNA-Seq Germline using Singularity Container

Tensorflow on O2

How to choose a partition in O2

Personal Python Packages

O2 Cluster Status

O2 Command CheatSheet

How to request or retain an O2 account

Rosetta License

Using Globus on O2

VS Code Server on O2

Optimizing O2 Jobs

Orientation for New O2 Cluster Users

Using (Local)ColabFold on O2

CheckPointing with DMTCP

HMS IT RC O2

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Personal R Packages

Created by Former user (Deleted)

Last updated: May 10, 2021 by Cox, Calvin D.

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