Install conda without license problems#

Here, we present three solutions for using the Conda package ecosystem without Anaconda license problems:

• Miniforge, a light version of Conda that uses conda-forge as its default package source (channel), which is free to use.
• Micromamba, a minimal version of Conda (actually, mamba, a Conda implementation in C++) that avoids any channel under the Anaconda license by default.
• Pixi, a lightweight package manager implementation that uses the Conda package ecosystem. It is free to use and open source.

For an overview of the different conda distribution see here.

Miniforge#

Download#

Conda is installed by downloading and executing an installer, but which version you need depends on your operating system.

Choose the appropriate installer from the list you can found here:
https://conda-forge.org/download/ or here https://github.com/conda-forge/miniforge.
Then copy the link and download the installer on your computer, see example below:

# Download Miniforge installer for 64-bit Linux
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O

# Download Miniforge installer for 64-bit Linux
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh 

Install#

Now you can execute the installer:

bash Miniforge3-Linux-x86_64.sh

The installer will ask you questions during the installation:

Press
Then press several times until reaching the next question.

• Do you accept the license terms?
  Yes
• Do you accept the installation path or do you want to choose a different one?
  Press
• Do you wish to update your shell profile to automatically initialize conda?
  Yes

Restart your shell so that the settings in ~/.bashrc or ~/.bash_profile can take effect. Or run

source ~/.bashrc 

You can verify that the installation worked by running:

conda --version

You can now get rid of the installer, you don't need it anymore

rm Miniforge3-Linux-x86_64.sh

Configure Channels#

Even if Miniforge only includes the conda-forge channel, which is free to use, it is always good to check the installation.

Check channels#

To verify the channels used by your installation you can type the following command:

conda config --show channels

You should see something like:

Add extra free channels#

You can add any free channel e.g. bioconda as follow:

conda config --add channels bioconda

Sharing environments safely#

For explanation why adding this extra line see here

conda config --add channels nodefaults

Reproducibility#

Is is recommended to set a strict channel priority.
It can dramatically speed up conda operations and also reduce package incompatibility problems.

conda config --set channel_priority strict

Auto activation#

By default conda will be activated to every new terminal you will open (in the base environment). To deactivate this behaviour run:

conda config --set auto_activate_base false

Micromamba#

Micromamba is a fully statically-linked, self-contained, executable. This means that the base environment is completely empty. The configuration for micromamba is slightly different, namely all environments and cache will be created by default under the MAMBA_ROOT_PREFIX environment variable. There is also no pre-configured .condarc/.mambarc shipped with micromamba (they are however still read if present).

Download and Install#

Micromamba is installed by downloading and executing an installer:

# Download Micromamba installer 
"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

The installer will ask you questions during the installation:

Press

Press

Press

Press

To take the changes into account restart your shell or run:

# (or ~/.bash_profile, ~/.zshrc, ~/.xonshrc, ~/.config/fish/config.fish, ...)
source ~/.bashrc 

You can verify that the installation worked by running:

micromamba --version

Configure Channels#

Even if Micromamba only includes the conda-forge channel, which is free to use, it is always good to check the installation.

Check channels#

To verify the channels used by your installation you can type the following command:

conda config --show channels

You should see something like:

Add extra free channels#

You can add any free channel e.g. bioconda as follow:

conda config --add channels bioconda

Sharing environments safely#

For explanation why adding this extra line see here

conda config --add channels nodefaults

Reproducibility#

Is is recommended to set a strict channel priority.
It can dramatically speed up conda operations and also reduce package incompatibility problems.

conda config --set channel_priority strict

Pixi#

Pixi provides thorough installation and setup instructions in its documentation. Review that documentation for the latest installation methods. For convenience, the typical methods follow.

For Linux and macOS, an installer is available:

curl -fsSL https://pixi.sh/install.sh | bash

or install with the pixi Homebrew formula:

brew install pixi

For Windows:

powershell -ExecutionPolicy ByPass -c "irm -useb https://pixi.sh/install.ps1 | iex"

To add channels to your project configuration in pixi.toml, use

pixi project channel add conda-forge