MicrobiomeGS2

constraint-based community metabolic modeling in R

MicrobiomeGS2 uses the approach of steadycom and ports it to methods implemented in R.

Installation

Using Conda

Install the conda dependencies within a new environment with the name MicrobiomeGS2.

wget https://raw.githubusercontent.com/Waschina/MicrobiomeGS2/master/requirements.yml
conda env create -f requirements.yml
rm requirements.yml
conda activate MicrobiomeGS2

Install the MicrobiomeGS2 package and dependencies required for SBML support

Rscript -e "devtools::install_github('Waschina/MicrobiomeGS2')"
wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz
R CMD INSTALL --configure-args=" \
--with-sbml-include=$CONDA_PREFIX/include \
--with-sbml-lib=$CONDA_PREFIX/lib" sybilSBML_3.1.2.tar.gz
rm sybilSBML_3.1.2.tar.gz

CPLEX support

Download and install cplex from the IBM homepage. Academic users can get a free licence for CPLEX and download the software for free. Get the cplexAPI package and link the library.

wget https://cran.r-project.org/src/contrib/Archive/cplexAPI/cplexAPI_1.4.0.tar.gz
R CMD INSTALL --configure-args=" \
   --with-cplex-dir=/path/to/cplex12.10/CPLEX_Studio/cplex" \
    cplexAPI_1.4.0.tar.gz
rm cplexAPI_1.4.0.tar.gz