Plugin for metabolic modeling of microbial communities.
Project description
A Qiime 2 plugin for MICOM.
Installation
This will become easier soon.
Setup Qiime 2
You will need a Qiime 2 environment with version 2020.2
or higher (how to install Qiime 2). For instance on Linux you would use:
wget https://data.qiime2.org/distro/core/qiime2-2020.2-py36-linux-conda.yml
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2020.2-py36-linux-conda.yml
Once installed, activate your Qiime 2 environment:
conda activate qiime2-2020.2
Install dependencies for q2-micom
from conda:
conda install -c conda-forge -c \
bioconda cobra umap-learn jinja2 loky pyarrow loguru tqdm
Install q2-micom
(this will install MICOM
as well).
pip install q2-micom
Install a QP solver
CPLEX
After registering and downloading the CPLEX studio for your OS unpack it (by running the provided installer) to a directory of your choice (we will assume it's called ibm
).
Now install the CPLEX python package:
pip install ibm/cplex/python/3.6/x86-64_linux
Substitute x86-64_linux
with the folder corresponding to your system (there will only be one subfolder in that directory).
Gurobi
Gurobi can be installed with conda.
conda install -c gurobi gurobi
You will now have to register the installation using your license key.
grbgetkey YOUR-LICENSE-KEY
Finish your installation
If you installed q2-micom
in an already existing Qiime 2 environment, update the plugin cache:
conda activate qiime2-2020.2 # or whatever you called your environment
qiime dev refresh-cache
You are now ready to run q2-micom
!
Usage
Here is a graphical overview of a q2-micom
analysis.
The best way to get started is to work through the community tutorial.
References
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
mSystems 5:e00606-19
https://doi.org/10.1128/mSystems.00606-19
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