Metadata-Version: 2.1
Name: orthofisher
Version: 0.0.2
Summary: orthofisher
Home-page: https://github.com/JLSteenwyk/orthofisher.git
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
License: UNKNOWN
Description: <p align="center">
          <a href="https://github.com/jlsteenwyk/orthofisher">
            <img src="https://raw.githubusercontent.com/JLSteenwyk/orthofisher/master/docs/_static/img/orthofisher.jpg" alt="Logo" width="400">
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          <p align="center">
            <a href="https://jlsteenwyk.com/orthofisher/">Docs</a>
            ·
            <a href="https://github.com/jlsteenwyk/orthofisher/issues">Report Bug</a>
            ·
            <a href="https://github.com/jlsteenwyk/orthofisher/issues">Request Feature</a>
          </p>
            <p align="center">
                <a href="https://lbesson.mit-license.org/" alt="License">
                    <img src="https://img.shields.io/badge/License-MIT-blue.svg">
                </a>
                <a href="https://pypi.org/project/orthofisher/" alt="PyPI - Python Version">
                    <img src="https://img.shields.io/pypi/pyversions/orthofisher">
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                <a href="https://github.com/JLSteenwyk/orthofisher/actions" alt="Build">
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                        alt="follow on Twitter">
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        </p>
        
        Orthofisher conducts automated and high-throughout identification of a predetermined set of orthologs, which can be used for phylgenomics, gene family 
        copy number determination and more!
        
        ---
        
        <br/>
        
        ## Quick Start
        
        For detailed instructions on usage and a tutorial, please see the [online documentation](https://jlsteenwyk.com/orthofisher/).
        
        <br/>
        
        ### 1) Prerequisite
        Before installing orthofisher, please first install [HMMER3](http://hmmer.org/documentation.html) and add the HMMER to your .bashrc path. For example, my .bashrc has the following:
        
        ```shell
        export PATH=$PATH:/home/steenwj/SOFTWARE/hmmer-3.1b2-linux-intel-x86_64/binaries
        ```
        
        <br/>
        
        ### 2) Install orthofisher
        
        **If you are having trouble installing orthofisher, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
        
        <br/>
        
        To install via *anaconda*, execute the follwoing command:
        ``` shell
        conda install -c jlsteenwyk orthofisher
        ```
        Visit here for more information: https://anaconda.org/jlsteenwyk/clipkit
        
        <br/>
        
        To install via *pip*, execute the follwoing command:
        ```shell
        pip install orthofisher
        ```
        
        <br />
        
        To install from source, execute the follwoing command:
        ```shell
        # download
        git clone https://github.com/JLSteenwyk/orthofisher.git
        # change dir
        cd orthofisher/
        # install
        make install
        ```
        
        <br/>
        
        If you run into software dependency issues, install orthofisher in a virtual environment. To do so, create your virtual environment with the following command: 
        ```shell
        # create virtual environment
        python -m venv .venv
        # activate virtual environment
        source .venv/bin/activate
        ```
        
        Next, install the software using your preferred method above. Thereafter, you will be able to use orthofisher.
        
        To deactivate your virtual environment, use the following command:
        ```shell
        # deactivate virtual environment
        deactivate
        ```
        **Note, the virtual environment must be activated to use *orthofisher*.**
        
        
        
        
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
