Demystifying Conda (Anaconda, Miniconda and Bioconda) and Virtual Environments

Рет қаралды 5,858

Күн бұрын

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:
github.com/kpatel427/KZbinT...
▸ Resources:
1. conda installation instructions: conda.io/projects/conda/en/la...
2. conda channels and priorities: angus.readthedocs.io/en/2019/...
3. Python virtual envs: / python-virtual-environ...
4. renv documentation: 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:
www.buymeacoffee.com/bioinfor...
To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: khushbu_p@hotmail.com
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Пікірлер: 19

@kedar_ghimire 10 күн бұрын

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

@ncedilemankahla9758 7 ай бұрын

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

@5602KK 7 ай бұрын

Great to have this as a resource

@PsycheSnacks657 7 ай бұрын

Always wonderful! Thank you

@sonunitjsr223 4 ай бұрын

Very useful

@ramachandran8106 7 ай бұрын

Useful video lesson.. 👍 Please upload GWAS data analysis..

@bahatilouch7420 4 ай бұрын

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!

@islamalmsarrhad2152 Ай бұрын

Thanks

@quinattasneemrafique536 5 ай бұрын

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

@paulcantalupo-nv1490 7 ай бұрын

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.

@AndrewBlakeOxford 7 ай бұрын

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.

@Bioinformagician 7 ай бұрын

You're absolutely right that when sharing a project, it's crucial to consider how the environment is set up for others who may not have previously used renv. Having renv activate and restore at the start is crucial. I'll update my script accordingly. Thank you for pointing that out!

@funnyarian 6 ай бұрын

But, there is that .Rprofile file that redirects to renv/activate.R which activates renv at the start? what's the reason to have it in the script?

@AndrewBlakeOxford 6 ай бұрын

Yeah we saw that too, we end up having to debug renv quite a bit when it starts being tricky so having the discrete steps in code makes it easier to re run/ double check etc. We also run R out into continuous integration gitlab dockers and wanted to be sure that each step is being run but you could probably get rid of the activate step and let it take take of itself.