Instructions on how to install on your local (Linux) machine. For HPC use, see here

Prerequisites

• Conda (Miniconda or Anaconda): How to install on linux instructions
• Python 3.7 or higher
• Access to the internet for downloading packages and databases.

Installing MetaPhlAn 4

Using conda

1. Install conda (if not already installed)instructions

   mkdir -p ~/miniconda3
   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
   bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
   rm -rf ~/miniconda3/miniconda.sh
   
   ## initialize your newly-installed Miniconda
   ~/miniconda3/bin/conda init bash
   

2. Create a conda environment for MetaPhlAn 4:

   conda create -y -n metaphlan4_env python=3.8
   conda activate metaphlan4_env
   

3. Install MetaPhlAn 4 using conda:

   conda install -c bioconda -c conda-forge metaphlan -y
   

4. To test installtion:

   metaphlan --version
   

Installing HUMAnN 3.0

Using conda

1. Install conda (if not installed).

2. Create a conda environment for HUMAnN 3.0:

   conda create -y -n humann3_env python=3.8
   conda activate humann3_env
   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --add channels biobakery
   

3. Install HUMAnN 3 using conda:

   conda install -y -c biobakery human
   

4. To test installation:

   humann --version
   humann_test