Demystifying Conda (Anaconda, Miniconda and Bioconda) and Virtual Environments
Today, we're diving into a topic that every developer, data scientist, or a bioinformatician has experienced at some point: the dreaded installation errors for conflicts due to package versions and dependency nightmare.
In this video, I'll walk you through the basics of setting up Conda and Renv. I talk about what's with the different condas - Anaconda, Miniconda and Bioconda. I'll show you how to create environments, install packages, and effortlessly switch between them. It's a game-changer for your coding and pipeline development journey!
I hope you find this video helpful! Leave your thoughts in the comment section below!
▸ Link to Code:
https://github.com/kpatel427/YouTubeT...
▸ Resources:
1. conda installation instructions: https://conda.io/projects/conda/en/la...
2. conda channels and priorities: https://angus.readthedocs.io/en/2019/...
3. Python virtual envs: / python-virtual-environments-tutorial-using...
4. renv documentation: https://rstudio.github.io/renv/articl...
Chapters:
0:00 Intro
0:51 What are virtual environments?
2:13 What is conda?
5:15 What’s with different condas - Anaconda, Miniconda and Bioconda?
7:15 renv vs conda
9:33 Demonstration goals and requirements
10:23 conda installation instructions
12:24 conda channels and priorities
13:44 Search for conda packages
14:36 base environment in conda
15:48 Checking local versions of the tools and searching for required conda packages
18:13 Create virtual environment in conda
22:03 Export environment to a YAML file (.yml file)
23:21 Create a conda environment from a YAML file
23:37 Why having a centralized location for all packages is problematic for analysis in R?
26:43 Creating R projects and using renv within projects
34:06 Sharing renv - save package version information to a .lock file
You can show your support and encouragement by buying me a coffee:
https://www.buymeacoffee.com/bioinfor...
To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
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