condacheat.md

Conda cheat sheet

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Managing environments

List all environments

$ conda info -e

Adding channels

via .condarc

$ cat ~/.condarc
ssl_verify: true
channels:
  - conda-forge
  - bioconda
  - defaults

Create a new environment

$ conda create --name <myenv> <package>=<version>
*OR*
$ conda env create -f environment.yml

Activating and Deactivating environments

$ conda activate <myenv> 
$ conda deactiavte <myenv>

Updateing an environment from environment.yml file

$ conda env update --prefix ./env --file environment.yml  --prune

The prune option removes any no longer needed dependencies

Removing an environment

$ conda remove --name <myenv> --all

To clean unnecessary cached files, tarballs, and stuff

$ conda clean --all

Export the environment

#Freeze the current environment into requirements.txt:
$ conda list --export > requirements.txt
#Freeze the current environment into environment.yml:
$ conda env export > environment.yml

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Example of environment.yml file

name: Environment name
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python=3.8
  - sample-sheet=0.12.0

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Set what to show on the command line prompt

These settings are made in the .condarc file, most often located in the home folder

changeps1 (bool)  
# When set to 'True', will change the command prompt ($PS1) to 
# include the activated environment.

env_prompt: '({default_env})'
# Template for prompt modification based on the active environment.
# Currently supported template variables are '{prefix}', '{name}', and
# '{default_env}'. '{prefix}' is the absolute path to the active
# environment. '{name}' is the basename of the active environment
# prefix. '{default_env}' holds the value of '{name}' if the active
# environment is a conda named environment ('-n' flag), or otherwise
# holds the value of '{prefix}'. Templating uses python's str.format()
# method.