Conda/Mamba

A Brief History

Bioinformatics research can be divided into pre-conda and post-conda eras. Before conda is developed, installing and running software developed by others was a big pain, due to different dependencies and system platforms.

Conda is the most popular software environment management platform on Linux/Mac/Windows. It has gained popularity due to its self-contained environment for software dependency and reproducibility. The default is Anaconda, and a minimal version is available as Miniconda.

A shortcoming for conda is that it can get extremely slow for resolving complex software and channel dependencies (yes, extremely = a few hours). Therefore, a faster version is developed and named as Mamba.

As of 2022, I strongly encourage everyone to use Mamba over Conda. They have the same functionalities, while Mamba is much faster.

Getting Mamba

We strongly recommend to start from mambaforge, a community project of the conda-forge community. However, if you already have conda installed before, you can also install mamba to its base environment.

You can download mambaforge for Windows, macOS and Linux.mambaforge comes with the popular conda-forge channel preconfigured, but you can modify the configuration to use any channel you like.

After successful installation, you can use the mamba commands as described in mamba user guide.

Managing Environments

• Try to use general environments, instead of one-software-one-environment.

• Use conda for installing packages by default; however, sometimes Pip is better, if you find conda finds unnecessary dependencies (that happens).