Conda Cheatsheet - Anaconda commandline parameters - most useful conda commands

Forgotten the conda command parameters?

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Here’s a Conda Cheatsheet I’ve compiled some time ago… This Conda Cheatsheet is covering the most essential commands and tips for managing environments, packages, and channels I’ve found useful.

Sleeping conda

Have a look at the uv - New Python Package, Project, and Environment Manager

Installing and Updating Conda

Verify Conda Installation and Version:
```
conda info
```
Update Conda:
```
conda update conda
```
Update Anaconda Meta Package:
```
conda update anaconda
```

Managing Environments

Create a New Environment:

conda create --name my_env
conda create -n my_env python=3.8  # Specify Python version
conda create -n bioinfo fastqc trimmomatic bwa  # Create with specific packages

Activate an Environment:

conda activate my_env  # On Windows, Linux, macOS
source activate my_env  # On Linux, OS X (older syntax)

Deactivate an Environment:
```
conda deactivate
```
List All Environments:
```
conda env list
conda info --envs
```

Clone an Environment:

conda create --clone old_env --name new_env

Rename an Environment:
```
conda env rename -n old_env -d new_env
```

Delete an Environment:

conda env remove -n my_env
conda remove --name my_env --all

List Revisions of an Environment:
```
conda list --revisions
```

Restore Environment to a Revision:

conda install --rev 3  # Roll back to revision 3

Managing Packages

List Installed Packages:

conda list
conda list -n my_env  # List packages in a specific environment

Install a Package:

conda install package_name
conda install -c conda-forge package_name  # Install from a specific channel
conda install package_name=1.2.3  # Install a specific version

Update All Packages in an Environment:
```
conda update --all
```

Uninstall a Package:

conda remove package_name
conda remove --name my_env package_name  # Uninstall from a specific environment

Search for Packages:

conda search package_name
conda search -c conda-forge package_name  # Search in a specific channel

Working with Channels

List Channels:
```
conda config --show channels
```

Add a Channel:

conda config --add channels conda-forge
conda config --prepend channels conda-forge  # Add with highest priority
conda config --append channels bioconda  # Add with lowest priority

Set Channel Priority:

conda config --set channel_priority strict

Exporting and Importing Environments

Export Environment to YAML:

conda env export > environment.yml
conda env export --from-history > environment.yml  # Export only explicitly asked packages

Import Environment from YAML:

conda env create --name my_env --file environment.yml

Export Environment to TEXT File:
```
conda list --export > requirements.txt
```

Import Environment from TEXT File:

conda create --name my_env --file requirements.txt

Additional Commands

Get Help for a Command:
```
conda -h
conda install -h
```
Clean Up Unused Files:
```
conda clean --all
```

Examine Conda Configuration:

conda config --get
conda config --get channels

Mamba (Optional)

Mamba is a faster alternative to Conda, but it has some limitations, especially regarding environment revisions.

Install Mamba:
```
conda install -c conda-forge mamba
```
Use Mamba Interchangeably with Conda: Most commands are the same, but Mamba does not support rolling back environment revisions[2][4].

Tips

Create Descriptive Environment Names: Helps in managing multiple environments.
Activate Environment Before Installing Packages: Ensures packages are installed in the correct environment.
Use Specific Channels for Packages: Ensures you get the packages from the desired sources.
Avoid Dependency Conflicts: Install all programs in the environment at the same time[5].