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:

▸ Resources:

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

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[kedar_ghimire]

this was really helpful for a non-bioinformatic researcher like me to understand whats going on. Especially the parts where you showed command by command to create two environments. Most of the youtube videos overestimate the programming skills of non-bioinformaticians and forget that it is them who watch these videos. Also, i like how you explain everything without missing even the minor stuff :D thanks

[kyounokuma]

What a fantastic overview of Conda. Thank you so much. You've answered all of my questions.

[ncedilemankahla]

Great timing on this video. I’m just getting started working in Conda and renv.. keep up the excellent work

[Iceletters]

thank you very much for this amazing video!! you help me a lot to understand how conda works!

[quinattasneemrafique]

Is it feasible to make a detailed overview on how to construct a Metagenomics pipeline?

[bahatilouch]

Great video and thank you for the tutorial! Would it be possible to make a tutorial about Virtual machines, cloud computing systems and docker?
Thank you so much again!

[AndrewBlakeOxford]

Renv linked the packages from your cache rather than installing them from fresh - this process won't be as quick for others who haven't already use renv to install them previously and hence won't be present in the renv cache . Your script would benefit from having the renv activate and restore code at the start else when you share it the project won't load and restore the environment. Great video - love your channel.

[kamalhasan-lgfl]

mam, i have installed conda, when i give conda show channels, bioconda is not installed, it is showing conda script py error

[ramachandran]

Useful video lesson.. 👍

Please upload GWAS data analysis..

[paulcantalupo-nv]

Thank you for the video. Very helpful. One suggestion though...your subtitles are blocking the code that you are trying to show. Thank you again.

[phoenix-xfyk]

Mam can you please guide me on how to install ascend

[VasaviKoneru]

Can you do a video on how to install cell ranger on linux?

[palakgupta]

hi are you still working as a scientist also at some lab?