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Transitioning Workflows to CyVerse: Tips & Tricks

Forest Carbon Codefest Data Storage

  • Path: ~/data-store/data/iplant/home/shared/earthlab/forest_carbon_codefest/
  • Your team has a subdirectory within the Team_outputs directory.

Setup

  1. CyVerse Account:
  2. Create an account if not already owned.
  3. Contact Tyson for account upgrades after maximizing current limits.

GitHub Connection

  • Follow the guide for connecting GitHub to CyVerse
  • Select “JupyterLab ESIIL” and choose “macrosystems” in the version dropdown.
  • Clone into /home/jovyan/data-store.
  • Clone innovation-summit-utils for SSH connection to GitHub.
  • Run conda install -c conda-forge openssh in the terminal if encountering errors.
  • GitHub authentication is session-specific.

RStudio in Discovery Environment

  1. Copy your instance ID. It can be found in your analyis URL in form https://.cyverse.run/lab.
  2. Use your ID in these links and run them each, in sequence, in the same browser window:
  3. https://<id>.cyverse.run/rstudio/auth-sign-in
  4. https://<id>.cyverse.run/rstudio/

Data Transfer to CyVerse

  • Use GoCommands for HPC/CyVerse transfers.
  • Installation:
  • Linux: GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \ curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-amd64.tar.gz | tar zxvf -
  • Windows Powershell: curl -o gocmdv.txt https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt ; $env:GOCMD_VER = (Get-Content gocmdv.txt) curl -o gocmd.zip https://github.com/cyverse/gocommands/releases/download/$env:GOCMD_VER/gocmd-$env:GOCMD_VER-windows-amd64.zip ; tar zxvf gocmd.zip ; del gocmd.zip ; del gocmdv.txt
  • Usage:
  • ./gocmd init
  • Hit enter until you are asked for your iRODS Username (which is your cyverse username)
  • Use put for upload and get for download.
  • Ensure correct CyVerse directory path. Note that the CyVerse directory path should start from “/iplant/home/…” (i.e. if you start from ‘/home/jovyan/…’ GoCommands will not find the directory and throw an error)
Last update: 2024-05-09