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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.


  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
  2. Use your ID in these links and run them each, in sequence, in the same browser window:
  3. https://<id>
  4. https://<id>

Data Transfer to CyVerse

  • Use GoCommands for HPC/CyVerse transfers.
  • Installation:
  • Linux: GOCMD_VER=$(curl -L -s; \ curl -L -s${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-amd64.tar.gz | tar zxvf -
  • Windows Powershell: curl -o gocmdv.txt ; $env:GOCMD_VER = (Get-Content gocmdv.txt) curl -o$env:GOCMD_VER/gocmd-$ ; tar zxvf ; del ; 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