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.

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Last update: 2024-05-24