What is Mamba

Posted on April 10, 2022

If you use conda, you should use mamba. What is mamba then? The website describes it as:

A Python-based CLI conceived as a drop-in replacement for conda, offering higher speed and more reliable environment solutions

So you install mamba into your conda environment and for certain commands where you would use conda you use mamba instead. The parameters are effectively the same.

So when you want to Create an enviroment:

conda create  -n myenv -c bioconda samtools
# becomes
mamba create -n myenv  -c bioconda  samtools

Install software:

conda install bqplot
# becomes
mamba install bqplot

Remove software:

conda remove bqplot
# becomes
mamba remove bqplot

As you can see, it's pretty much substitute conda for mamba. The outcome is exactly the same, except the install time is much faster.

I usually keep seperate enviroments for each project, so I first create the enviroment with conda with mamba installed and then I switch to using mamba like the examples above. e.g.

conda create  -n myenv mamba
conda activate myenv
mamba install prokka