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This tutorial is available for download as a PDF here.

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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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