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Conda

setup Conda and Mamba on WSL Ubuntu

  • download the .sh files from the websites corresponding to Linux
  • run bash Miniconda....sh
  • allow the init to occur to copy the relevant source to .bashrc
  • otherwise later you can do source ~/miniconda3/etc/profile.d/conda.sh and then conda init
  • same thing with mamba basically

Environments

General commands

conda create --name py35 python=3.7
conda activate py35
conda deactivate
conda list
conda env remove --name bio-env

List all environments

conda info --envs
conda info -e

List revisions

conda list --revisions
conda install --revision 2

Requirements files

One way is to create a text file

conda list --explicit > bio-env.txt
conda env create --file bio-env.txt

Or a YAML file:

conda env export > environment.yml

Channels

Conda Forge

conda config --add channels conda-forge 
conda config --set channel_priority strict 
conda install <package-name>

source

Channel priority

As of version 4.6.0, Conda has a strict channel priority feature. Strict channel priority can dramatically speed up conda operations and also reduce package incompatibility problems. We recommend it as a default. However, it may break old environment files, so we plan to delay making it conda's out-of-the-box default until the next major version bump, conda 5.0: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html

How to set

conda config --describe channel_priority
conda config --set channel_priority strict

source

Setting up on Git Bash

. /c/Users/<username>/AppData/Local/Continuum/anaconda3/etc/profile.d/conda.sh
conda init bash

Cheat sheets

https://docs.conda.io/projects/conda/en/4.6.0/\_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf https://kapeli.com/cheat\_sheets/Conda.docset/Contents/Resources/Documents/index