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HMS IT RC O2

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Published Papers That Used O2, Orchestra, or Research Computing
Report CPU/Mem usage in slurm job standard output
Text for Grants Referring to the HMS Research Cluster
Troubleshooting Slurm Jobs
Filesystems
Security on O2
Moving from Orchestra to O2
Using Mathematica on O2
sratoolkit/2.10.7 to download NCBI SRA data
Using O2 GPU resources
Scratch_gpu Storage
771 Open Source Applications on O2 [BioGrids]
Using Slurm Basic
File Transfer
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
Over Efficient Jobs
sratoolkit/2.10.7 to download dbGAP data
Jupyter on O2
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
Juicer
Using AlphaFold on O2
Using MATLAB
Frequently Asked Questions and Answers
tmux: Keep Linux Sessions Alive (so you can go back to the same terminal window from anywhere, anytime)
Two Factor Authentication FAQ
How to troubleshoot the sratoolkit/2.10.7 module
RC workflows
UCSC Genome Browser and IGV access for data on O2
Running Singularity Containers in O2
Using Java on O2
GATK4 Mutect2 using Singularity Container
Job Priority
O2 HPC Cluster and Computing Nodes Hardware
Currently Available Software on O2
How to login to O2
Personal R Packages
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
Conda on O2
O2 Cluster Status
O2 Command CheatSheet
How to request or retain an O2 account
Rosetta License
Using Globus on O2
VSCode and Code Server on O2
Optimizing O2 Jobs
Orientation for New O2 Cluster Users
Using (Local)ColabFold on O2
CheckPointing with DMTCP
O2Portal
OpenFold On O2
Protein Structure Prediction on O2
Installing LocalColabFold Locally
Improving O2 Efficiency by Changing User Priority
Deleting Files from a Directory on O2 After Hitting the Storage Limit
Querying O2 Filesystem Quota Usage
Installing OpenFold Locally on O2
RStudio on O2
How to connect to your sbatch running job
Installing Difficult Conda Packages on O2
Helpful Tips and Tricks
Shared Containers on O2
Smart Slurm: Dynamic and accurate resource allocation for O2 jobs
RoseTTAFold All-Atom on O2
Nextflow (`nf-core`) on O2
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Owned by Gaby Rodriguez

Mar 05, 2025

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