Metadata-Version: 2.1
Name: q2-micom
Version: 0.7.1
Summary: Plugin for metabolic modeling of microbial communities.
Home-page: https://github.com/micom-dev/q2-micom
Author: Christian Diener
Author-email: cdiener@isbscience.org
License: Apache License 2.0
Description: <img src="docs/assets/logo.png" width="75%">
        
        ![Python package](https://github.com/micom-dev/q2-micom/workflows/Python%20package/badge.svg)
        [![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
        
        *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](https://docs.qiime2.org/2020.2/install/native/#install-qiime-2-within-a-conda-environment)). For instance on Linux you would use:
        
        ```bash
        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:
        
        ```bash
        conda activate qiime2-2020.2
        ```
        
        Install dependencies for `q2-micom` from conda:
        
        ```bash
        conda install -c conda-forge -c \
            bioconda cobra umap-learn jinja2 loky pyarrow loguru tqdm
        ```
        
        Install `q2-micom` (this will install `MICOM` as well).
        
        ```bash
        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:
        
        ```bash
        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.
        
        ```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 qiime2-2020.2  # 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.
        
        <img src="docs/assets/overview.png" width="100%">
        
        The best way to get started is to work through the [community tutorial](https://github.com/micom-dev/q2-micom/blob/master/docs/README.md).
        
        ## 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
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: test
