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Using Mamba to install Conda packages

Mamba is an alternative to Conda package manager. The main advantage is its speed regarding dependency resolution.

Setting up Mamba

The proposed installation is based on micromamba and doesn't require any installation or module loading on the cluster. You just have to add the following 2 lines to your ~/.bashrc file:

export PATH="$PATH:/dcsrsoft/spack/external/micromamba"

Of course, replace /work/FAC/INSTITUTE/PI/PROJECT with the path corresponding to your project.

Then, you just have to run the initialization process with the following command:

micromamba shell init

Finally, you have to logout from the cluster and the environment will be properly configured at the next login.

Using Mamba

Instead of using conda commands, you can replace conda with micromamba. For instance:

micromamba create --prefix ./my_mamba_env
micromamba activate ./my_mamba_env
micromamba install busco -c conda-forge -c bioconda
busco -v
micromamba deactivate


You cannot use Mamba with virtual environment created previously with Conda. Such environments must be recreated.