Installation

Linux OS

1. Download Biomix from the GitHub page: https://github.com/IxI-97/BiomiX2.2/releases/download/v2.2/BiomiX2.2.zip and decompress it. The installation in the home directory is suggested. From bash type

   cd
   wget https://github.com/IxI-97/BiomiX2.2/releases/download/v2.2/BiomiX2.2.zip
   tar -xvzf Biomix2.2.tar.gz
   

2. BiomiX uses conda to install the R and Python package dependencies. Install conda from the website: https://docs.conda.io/en/latest/miniconda.html or type on the bash

   wget https://repo.anaconda.com/miniconda/Miniconda3-py310_23.3.1-0-Linux-x86_64.sh
   bash Miniconda3-py310_23.3.1-0-Linux-x86_64.sh
   

3. Follow the instructions, selecting conda init = yes. Close and reopen the bash terminal.
4. Create your BiomiX environment (BiomiX-env) in conda typing on the bash

   conda create -n BiomiX-env python=3.9 r-base=4.2.0 r-essentials
   

5. Activate your BiomiX environment

   conda activate BiomiX-env
   

6. Run the BiomiX_INSTALL Python script

   python3 path/to/BiomiX2.2/_INSTALL/BiomiX_INSTALL.py
   

7. Enjoy BiomiX!

Windows OS

1. Download Biomix from the GitHub page and decompress it (by application e.g. Winzip or terminal cmd). The installation in the home directory is suggested. If using the Windows terminal type

   cd
   wget linktothelatestBiomiXversion
   tar -xvzf Biomix2.2.tar.gz
   

2. BiomiX uses conda to install the R and Python package dependencies. Install conda from the website https://docs.conda.io/en/latest/miniconda.html
3. Follow the installation instructions
4. Open the search in the Windows taskbar for the application "Anaconda powershell prompt"
5. Create your BiomiX environment (BiomiX-env) in conda typing on the conda PowerShell

   conda create -n BiomiX-env python=3.9
   

6. Activate your BiomiX environment

   conda activate BiomiX-env
   

7. Install the R and igraph package.

   conda install -c conda-forge r-base=4.1.3
   conda install -c conda-forge r-igraph
   

8. Run the BiomiX_INSTALL Python script by clicking on it or typing in the conda PowerShell

   python path/to/BiomiX2.2/_INSTALL/BiomiX_INSTALL.py
   

9. Enjoy BiomiX!