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Introduction: This workshop will introduce what Conda is and how it can be used to create a variety of environments, such as Python/R and contained applications.

Course Goals:

  1. Introduce Conda and what it is good for, and how to use on ARCC’s clusters.

  2. How to use Conda to create a variety of environments - based on Python, R and standalone applications.

  3. Detail some of the core Conda configurations that affect your environment.

Notes:

  • This workshop focuses purely on using Conda. We have a more advanced workshops that details the interplay between Python, Conda and Pip.

  • If you have existing Conda environments, or have installed your own version of Anaconda, then the examples within this workshop might provide different results.

  • We have tried to make the examples as generic as possible. You will need to replace <project-name> and <username> with appropriate values that apply to you.

This tutorial is available for download as a PDF here.

Sections

  1. What is Conda? Using Miniconda3 on the Cluster: Introduce conda, define some terminology, how to use on the cluster and finding help.

  2. Example 01: Python, Numpy and Pandas Environment: Demonstrate a basic conda environment creation workflow by creating a Python environment that contains the numpy and pandas packages.

  3. Conda Configuration and Environments: Understand some of the basic conda configurations and where environments are stored.

  4. Example 02: R and TidyVerse: Create an environment using the R language that includes the TidyVerse library.

  5. Conda Channels: What are channels and how can they be used and configured.

  6. Example 03: Applications: SLiM: Demonstrate using conda to install a command-line application.

  7. Reproducibility and Sharing: Introduce how conda environments can be reproduced and shared.

  8. Example 04: Application: Qiime Ecosystem: Demonstrate importing the large qiime application ecosystem.

  9. Conda with salloc and sbatch: Demonstrate best practices using Conda environments with salloc and sbatch.

  10. Conda Workshop: Summary: Summarize the concepts covered across the workshop.

 

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