Conda Cheatsheet

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

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].