Metadata-Version: 2.1
Name: q2-micom
Version: 0.12.0
Summary: QIIME 2 plugin for metabolic modeling of microbial communities.
Home-page: https://github.com/micom-dev/q2-micom
Author: Christian Diener
Author-email: mail@cdiener.com,
License: Apache License 2.0
Description: <img src="https://github.com/micom-dev/q2-micom/raw/master/docs/assets/logo.png" width="75%">
        
        [![Test and deploy](https://github.com/micom-dev/q2-micom/actions/workflows/test_package.yml/badge.svg)](https://github.com/micom-dev/q2-micom/actions/workflows/test_package.yml)
        [![codecov](https://codecov.io/gh/micom-dev/q2-micom/branch/master/graph/badge.svg)](https://codecov.io/gh/micom-dev/q2-micom)
        [![PyPI version](https://badge.fury.io/py/q2-micom.svg)](https://badge.fury.io/py/q2-micom)
        
        
        A QIIME 2 plugin for MICOM.
        
        ## Installation
        
        You will need an existing QIIME 2 environment. Follow the instructions on ([how to install QIIME 2](https://docs.qiime2.org/2021.2/install/native/#install-qiime-2-within-a-conda-environment))
        otherwise. Let's assume that environment was called `qiime2-2021.2` 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.
        
        ```bash
        wget https://raw.githubusercontent.com/micom-dev/q2-micom/master/q2-micom.yml
        conda env update -n qiime2-2021.2 -f q2-micom.yml
        # OPTIONAL CLEANUP
        rm q2-micom.yml
        ```
        
        Finally, you activate your environment.
        
        ```bash
        conda activate qiime2-2021.2
        ```
        
        ### 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:
        
        ```bash
        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.
        
        ```bash
        conda install -c gurobi gurobi
        ```
        
        You will now have to register the installation using your license key.
        
        ```bash
        grbgetkey YOUR-LICENSE-KEY
        ```
        
        ### Finish your installation
        
        If you installed `q2-micom` in an already existing QIIME 2 environment, update the plugin cache:
        
        ```bash
        conda activate qiime2-2021.2  # 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.
        
        <img src="https://github.com/micom-dev/q2-micom/raw/master/docs/assets/overview.png" width="100%">
        
        The best way to get started is to work through the [community tutorial](https://micom-dev.github.io/q2-micom).
        
        ## Supported QIIME 2 versions
        
        `q2-micom` is tested against:
        
        1. the current [QIIME 2 version](https://docs.qiime2.org/)
        2. the previous version
        
        It should also work with
        
        3. the [development version](https://dev.qiime2.org/latest/)<br>
           However, this may occasionally break. Check [here for the current status](https://github.com/micom-dev/q2-micom/actions/workflows/qiime_dev.yml).
        
        
        ## References
        
        MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota <br>
        Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio <br>
        mSystems 5:e00606-19 <br>
        https://doi.org/10.1128/mSystems.00606-19
        
Keywords: microbiome,modeling,metabolism,community
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Description-Content-Type: text/markdown
