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HMS IT RC O2
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  • Moving from Orchestra to O2
  • Using Mathematica on O2
  • sratoolkit/3.2.0 to download NCBI SRA data
  • Scratch_gpu Storage
  • 795 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
  • 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
  • Understanding O2 Slurm Accounts/Associations and Unix Accounts/Groups
  • Using AlphaFold 2 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
    • Bwa through rcbio
    • Bowtie2 through rcbio
    • HTSeq through rcbio
    • Kallisto And Sleuth For RNASeq through rcbio
    • rsem-1.3.3 with bowtie-2.5.4
    • skewer, FastQC, Hisat2, Stringtie and Ballgown through rcbio
    • screen: Keep Linux Sessions Alive (so you can go back to the same terminal window from anywhere, anytime)
    • skewer, FastQC, Hisat2 and HtseqCount through rcbio/1.1
    • STAR through rcbio
    • Cutadapt, Bowtie2 and MACS2 for ChipSeq
    • skewer, FastQC, Hisat2 and HtseqCount through rcbio
    • Build Folder Structures From Sample Sheet for rcbio NGS Workflows new
    • Run Bash Script As Slurm Pipeline through rcbio
  • UCSC Genome Browser and IGV access for data on O2
  • Running Singularity Containers in O2
  • Using Java on O2
  • 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
  • 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
  • VSCode and Code Server on O2
  • Optimizing O2 Jobs
  • Orientation for New O2 Cluster Users
  • Using (Local)ColabFold on O2
  • CheckPointing with DMTCP
  • O2Portal
  • 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
  • RCBot
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