Installation and Usage

Linux OS

Download Biomix here: https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip and decompress it. Installation in the Desktop directory is strongly recommended.


Bash terminal commands
cd
wget https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip
unzip -q Biomix2.4.zip

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

Follow the instructions, selecting conda init = yes. Close and reopen the bash terminal.

Run the BiomiX_INSTALL_LINUX.sh script within the _INSTALL folder and wait until the end of the installation.

./path/to/BiomiX2.4/_INSTALL/BiomiX_INSTALL_LINUX.sh

Run the Biomix_exe.sh script within the BiomiX2.4 folder to open BiomiX and start your analysis.

./path/to/BiomiX2.4/Biomix_linux_exe.sh

Enjoy BiomiX!

Windows OS

Download Biomix https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip and decompress it. Installation in the home directory is strongly recommended.


Windows terminal commands
cd
wget https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip
Unzip the Biomix2.4.zip file.

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

Follow the installation instructions

Double-click in the BiomiX_INSTALL_WINDOWS.bat script within the _INSTALL folder and wait until the end of the installation.

Double-click on the Biomix_exe.bat script within the BiomiX2.4 folder to open BiomiX and start your analysis.

Enjoy BiomiX!

Mac-OS "Beta-version"

Download Biomix here: https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip and decompress it (by application e.g. Winzip or terminal cmd). Installation in the home directory is strongly recommended.


MAC OS terminal commands
cd
wget https://github.com/IxI-97/BiomiX/releases/download/v2.4/BiomiX2.4.zip
Unzip the Biomix2.4.zip file

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

Follow the installation instructions

Installation CMake on the Mac OS device CMake installation instructions

Open the terminal and run the following lines


/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh) #Installation brew
conda create -n BiomiX-env python=3.9 -y #Create BiomiX environment
conda activate BiomiX-env #Activation conda environment
conda config --add channels conda-forge #Add forge channel to conda repositories
conda install -c conda-forge r-base=4.4.1 -y #Installation R
conda install conda-forge::glib=2.82.1 -y #Installation glib
brew install libgit2 #installation litgit2
python3 /your/path/to/BiomiX2.4/_INSTALL/BiomiX_INSTALL_OS.py #Start the automatic installation.

Run the BiomiX_INSTALL_OS.sh script within the _INSTALL folder and wait until the end of the installation.

Run the Biomix_macos_exe.sh script within the BiomiX2.4 folder to open BiomiX and start your analysis.

./path/to/BiomiX2.4/Biomix_macos_exe.sh

Enjoy BiomiX!

Important notes: The MacOS beta version is less stable than linux and windows version because of the differences among MacOS M1/M2 and Intel version. Please help us to report any bug to improve the MacOS installation here: GitHub issues BiomiX or by mail to cristian.iperi@univ-brest.fr. BiomiX is actively implemented, so we answer quickly :)

Troubleshooting

ModuleNotFoundError: No module named 'package name'

It happens during the conda installation "step 2" because the Python installed on your computer doesn't have it. This can be fixed by typing in the terminal: pip install 'package name'

Error in library ("Package"): No package named "Package"

BiomiX uses Conda plus R packages from the github repositories to ensure a close virtual environment to avoid error because of package updated. Unfortunately some package in LinuX or MACOS installation can fail because of external libraries to install in the terminal. To solve this error is possible to open the R environment within the conda BiomiX-environment


Open the MAC-OS/Windows/Linux terminal and insert these commands
conda activate BiomiX-env #Activates the conda environment
R (Linux-MacOS) or R.exe (windows) #it opens the R environment
install.packages("Package") #Function to attempt the package installation 
library("Package") #Loading the installed package

If the install.packages or the library functions drive errors. The missing package or library will be displayed in the error message. As R packages rely on other R packages to work, it is important to detect the dependency failing the installation to solve it.


Error output example
Error in library ("tidyverse"): No package named "tidyverse"
Action: Open the R Conda BiomiX environment as previously mentioned

install.packages("devtools")
Output.: Error: dependency 'ragg' is not available for package tidyverse'
                        
install.packages("ragg")
Output:  Error: dependency 'systemfonts' is not available for package ragg'

install.packages("systemfonts")
Output: Configuration failed to find the fontconfig freetype2 library. Try installing:
deb: libfontconfig1-dev (Debian, Ubuntu, etc)
rpm: fontconfig-devel (Fedora, EPEL)
csw: fontconfig_dev (Solaris)
brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
:1:10: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.

Solution:  brew install freetype (MacOS), sudo apt-get install libfontconfig1-dev (Debian, Ubuntu, etc)