A Mamba installs

A.1 Mamba installation and environment

Mamba is a reimplementation of conda. It is a great tool for installing bioinformatic packages including R packages.

Mamba github: https://github.com/mamba-org/mamba

The best way to use Mamba is to install Miniforge. It has both Conda and Mamba commands.

Miniforge installation: https://github.com/conda-forge/miniforge

Mamba guide: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html

To create the mamba environment meta_barcode run the below commands in your bash. You will need to have installed mamba first.

#meta_barcode
mamba create -n meta_barcode
mamba activate meta_barcode
#Install packages from bioconda channel
mamba install -c bioconda bioconductor-dada2 bioconductor-biostrings bioconductor-shortread \
cutadapt bioconductor-phyloseq bioconductor-deseq2 blast megan
#Install packages from conda-forge channel
mamba install -c conda-forge r-vegan r-ggplot2 r-irkernel

A.2 Jupyter-notebook

If you are running this on your own computer you can use RStudio. However, you can also use Jupyter-notebook if you are using an HPC or prefer it.

If using bash you will need to create an environment with Jupyter-notebook. Ensure you are in the (base) mamba environment.

mamba create -n jupyter
mamba activate jupyter
mamba install -c anaconda jupyter
mamba deactivate

To run Jupyter-notebook with your meta_barcode environment you can run the following.

#Activate you meta_barcode env
mamba activate meta_barcode
#Run jupyter-notebook (may be a slightly different path)
~/mamba/envs/jupyter/bin/jupyter-notebook