Wanglab Cluster

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Dashboard

Quickly check node availability, job status and general usage statistics.

lets go !

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Available Software

We use modules for all common software. These are preinstalled and readily available to use.
Feel free to request specific tools and their versions to be added to the module system via slack.

You are welcome to have your own conda or micromamba installed for your useraccounts under /scratch/devtools/USERNAME. This is very useful for self-managing softwares that are available in any of the conda channels. We recommend using micromamba as it is fast, free and easy to install. see installation instructions below.

• List available software: module avail
• Softwares Overview: module overview
• Loading a module: module load samtools
• Unloading a module: module unload samtools
• List modules currently loaded: module

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Micromamba Installation

Quickly check cluster availability, job status and general usage statistics.

• cd /scratch/devtools/your-username/
• mkdir micromamba
• cd micromamba
• curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj
• cd bin
• micromamba shell init -s bash

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Slurm Batch script

Template for using many available software modules.

      #!/bin/bash -l
      #SBATCH --job-name=Sbatch-Test
      #SBATCH --partition=general
      #SBATCH --nodes=1
      #SBATCH --ntasks-per-node=1
      #SBATCH --cpus-per-task=1
      #SBATCH --time=0:05:00
      #SBATCH --output=./sbatch-test.log
      #SBATCH --error=./sbatch-test.err
      #SBATCH --mem=1G

      # load one or more available software modules 
      module load samtools java/11.0.2 

      ###
      ###
      ###
      # You actual code or job related script goes here
      ###
      ###
      ###

      # uncomment below and add your slack userid to receive a notification on slack once the job completes. (still in beta testing)
      # slurmbot your-slack-userid "Slurm job \`$SLURM_JOB_NAME\` with jobID : \`$SLURM_JOB_ID\` finished !"

    

Template for activating custom environments and slack notifications.

      #!/bin/bash -l
      #SBATCH --job-name=Sbatch-Test
      #SBATCH --partition=general
      #SBATCH --nodes=1
      #SBATCH --ntasks-per-node=1
      #SBATCH --cpus-per-task=1
      #SBATCH --time=0:05:00
      #SBATCH --output=./sbatch-test.log
      #SBATCH --error=./sbatch-test.err
      #SBATCH --mem=1G


      # if you are using micromamba for software environments
      # uncomment below line to enable micromamba within sbatch scripts
      # eval "$(micromamba shell hook --shell bash)"
      
      # activate your required environments
      # micromamba activate demo

      ###
      ###
      ###
      # You actual code or job related script goes here
      ###
      ###
      ###

      # uncomment below and add your slack userid to receive a notification on slack once the job completes. (still in beta testing)
      # slurmbot your-slack-userid "Slurm job \`$SLURM_JOB_NAME\` with jobID : \`$SLURM_JOB_ID\` finished !"

    

For details on slurm sbatch options and explanations go here.
We also maintain a wiki page for common usecases and code snippets here.

Request interactive slurm sessions using below command

srun --nodes=1 --ntasks-per-node=1 --time=00:10:00 --ntasks-per-node=1 --cpus-per-task=5 --mem=5G --pty bash -i

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Wangcluster Hosting Services

Host trackhubs and websites from Wangcluster.

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Rstudio

Quickly launch Rstudio sesssions.

• Start by adding rstudio to your PATH: export PATH="$PATH:/wanglab/rstudio/"
• Start a session by typing: rstudio
• To customize your rstudio session (password, threads, memory, etc), read the docs: rstudio -h

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