HMS IT RC O2

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Get information about current and past jobs
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Scratch Storage
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Filesystem Quotas
User Training
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Submitting data to GEO
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Published Papers That Used O2, Orchestra, or Research Computing
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Report CPU/Mem usage in slurm job standard output
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Text for Grants Referring to the HMS Research Cluster
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Troubleshooting Slurm Jobs
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Filesystems
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Security on O2
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Moving from Orchestra to O2
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Using Mathematica on O2
The O2 Open OnDemand Pilot
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sratoolkit/2.10.7 to download NCBI SRA data
Using O2 GPU resources
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Scratch_gpu Storage
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766 Open Source Applications on O2 [BioGrids]
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Using Slurm Basic
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File Transfer
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Get more informative slurm email notification
Local Software Installs
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Batch small jobs together as a big job
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UNIX Permissions Tutorial
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Using X11 Applications Remotely
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Public Databases
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Over Efficient Jobs
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sratoolkit/2.10.7 to download dbGAP data
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Jupyter on O2
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spp (1.15.2) for Chip-Seq
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O2 cron service
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How To Submit Parallel Jobs in O2
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Personal Perl Packages
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Using Aspera to Download Data
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Get more informative slurm email notification and logs through rcbio/1.3.3
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Understanding O2 Slurm Accounts/Associations and Unix Accounts/Groups
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Juicer
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Using AlphaFold on O2
Using MATLAB
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Frequently Asked Questions and Answers
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tmux: Keep Linux Sessions Alive (so you can go back to the same terminal window from anywhere, anytime)
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Two Factor Authentication FAQ
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How to troubleshoot the sratoolkit/2.10.7 module
RC workflows
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UCSC Genome Browser and IGV access for data on O2
Running Singularity Containers in O2
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Using Java on O2
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GATK4 Mutect2 using Singularity Container
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Job Priority
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O2 HPC Cluster and Computing Nodes Hardware
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Currently Available Software on O2
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How to login to O2
Personal R Packages
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How to Generate SSH Keys
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Using Applications on O2
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GATK4 RNA-Seq Germline using Singularity Container
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Tensorflow on O2
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How to choose a partition in O2
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Personal Python Packages
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Conda on O2
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O2 Cluster Status
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O2 Command CheatSheet
How to request or retain an O2 account
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Rosetta License
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Using Globus on O2
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VSCode and Code Server on O2
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Optimizing O2 Jobs
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Orientation for New O2 Cluster Users
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Using (Local)ColabFold on O2
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CheckPointing with DMTCP
O2Portal
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OpenFold On O2
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Protein Structure Prediction on O2
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Installing LocalColabFold Locally
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Improving O2 Efficiency by Changing User Priority
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Deleting Files from a Directory on O2 After Hitting the Storage Limit
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Querying O2 Filesystem Quota Usage
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Installing OpenFold Locally on O2
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RStudio on O2
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How to connect to your sbatch running job
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Installing Difficult Conda Packages on O2
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Helpful Tips and Tricks
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Shared Containers on O2
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Smart Slurm: Dynamic and accurate resource allocation for O2 jobs
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RoseTTAFold All-Atom on O2
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Nextflow (`nf-core`) on O2

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GATK4 RNA-Seq Germline using Singularity Container

GATK4 RNA-Seq Germline using Singularity Container

Owned by Lingsheng Dong

Last updated: Dec 11, 2023

8 min read

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