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
export PATH="$PATH:/dcsrsoft/spack/external/micromamba" export MAMBA_ROOT_PREFIX="/work/FAC/INSTITUTE/PI/PROJECT/mamba_root"
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.
Instead of using
conda commands, you can replace
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.