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QIIME 2 plugin for metabolic modeling of microbial communities.

Project description

Test and deploy codecov PyPI version

A QIIME 2 plugin for MICOM.

Installation

You will need an existing QIIME 2 environment. Follow the instructions on (how to install QIIME 2) otherwise. Let's assume that environment was called qiime2-2021.8 for all further steps.

Add q2-micom to the QIIME 2 environment

This will be the same step for any supported QIIME 2 version or operating systems.

wget https://raw.githubusercontent.com/micom-dev/q2-micom/master/q2-micom.yml
conda env update -n qiime2-2021.8 -f q2-micom.yml
# OPTIONAL CLEANUP
rm q2-micom.yml

Finally, you activate your environment.

conda activate qiime2-2021.8

Install a QP solver (optional)

q2-micom will now install the open source solver OSQP that can be used with MICOM. OSQP is fairly fast and will give solutions with accuracy in the order of 1e-3 - 1e-4. If you use MICOM regularly we do recommend to obtain an academic license for CPLEX which will be faster and more accurate. We do not recommend Gurobi anymore because we can not test it as stringently as the other solvers and it is also slower than CPLEX or OSQP. However, you may still use Gurobi with q2-micom, but things may break.

CPLEX (recommended)

QIIME 2 versions before 2021.4 are only compatible with CPLEX 12.10 or earlier (later version require at least Python 3.7).

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 into your activated environment:

pip install ibm/cplex/python/3.6/x86-64_linux

Substitute 3.6 with the Python version in your QIIME 2 environment, 3.6 for QIIME 2 up to 2021.2 and 3.8 for QIIME 2 2021.4 and newer. Substitute x86-64_linux with the folder corresponding to your system (there will only be one subfolder in that directory).

Gurobi (works, but not recommended)

q2-micom is not tested against Gurobi. Consequently Gurobi support is often iffy and might break for periods of time. It will also be much slower than CPLEX or OSQP.

You should only consider using Gurobi if:

  1. You do not have access to CPLEX
  2. You do need high accuracy solutions (tolerance of 1e-6 or lower)

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 qiime2-2021.8  # 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.

Supported QIIME 2 versions

q2-micom is tested against:

  1. the current QIIME 2 version
  2. the previous version

It should also work with

  1. the development version
    However, this may occasionally break. Check here for the current status.

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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