Versions Compared

Old Version 30

changes.mady.by.user Simon Alexander

Saved on

compared with

New Version Current

changes.mady.by.user Simon Alexander

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  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.

...

Warning

20240911: Currently, across many HPC centers, there are discussions and some confusion over the academic license terms for using miniconda3.

This is being reviewed by Anaconda.com, and we are awaiting clarity on the issue.

Depending on the outcome we might move to using miniforge, instead of miniconda3.

The concepts and context of this workshop should not change, just the name of the module that will need to be loaded.

...

Note

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

  • 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

modify user and project names to apply to yourself

  • 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: FAQs: A list of commonly asked questions that will be addressed here, but not necessarily within the workshop itself.

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

...