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Transitioning Workflows to CyVerse: A Guide for ESIIL Postdocs

Earth Lab Data Storage

  • Path: /home/jovyan/data-store/iplant/home/shared/earthlab/
  • Ensure your project has a directory within the Earth Lab data storage.

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 Elsa Culler's 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 DE

  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:
  3. https://<id>.cyverse.run/rstudio/auth-sign-in
  4. https://<id>.cyverse.run/rstudio/

Package Requests

  • List desired packages here for future container updates.

Data Transfer to CyVerse

  • Use GoCommands for HPC/CyVerse transfers.
  • Installation:
  • Linux: (Command)
  • Windows Powershell: (Command)
  • Usage:
  • Use put for upload and get for download.
  • Ensure correct CyVerse directory path.

Last update: 2024-05-12