Metadata-Version: 2.1
Name: phables
Version: 0.1.0a3
Summary: Phables: Phage bubbles resolve bacteriophage genomes in viral metagenomic samples
Home-page: https://github.com/Vini2/phables
Author: Vijini Mallawaarachchi
Author-email: viji.mallawaarachchi@gmail.com
License: MIT
Description: <p align="center">
          <img src="https://raw.githubusercontent.com/Vini2/phables/master/phables_logo.png" width="600" title="phables logo" alt="phables logo">
        </p>
        
        Phables: Phage bubbles resolve bacteriophage genomes in viral metagenomic samples
        ===============
        
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        Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data. It models cyclic phage-like components in the viral metagenomic assembly as flow networks, models as a minimum flow decomposition problem and resolves genomic paths corresponding to flow paths determined. Phables uses the [Minimum Flow Decomposition via  Integer Linear Programming](https://github.com/algbio/MFD-ILP) implementation to obtain the flow paths.
        
        For detailed instructions on installation and usage, please refer to the [**documentation hosted at Read the Docs**](https://phables.readthedocs.io/en/latest/).
        
        **NEW:** Phables is now available on Anaconda.org at [https://anaconda.org/vijinim/phables](https://anaconda.org/vijinim/phables) and on PyPI at [https://pypi.org/project/phables/](https://pypi.org/project/phables/). Feel free to pick your package manager.
        
        <p align="center">
          <img src="https://raw.githubusercontent.com/Vini2/phables/master/Phables_workflow.png" title="phables workflow" alt="phables workflow">
        </p>
        
        ## Setting up Phables
        
        ### Option 1: Installing Phables from Anaconda.org
        
        You can install Phables from Anaconda.org at [https://anaconda.org/vijinim/phables](https://anaconda.org/vijinim/phables).
        
        ```bash
        # add channels
        conda config --add channels defaults
        conda config --add channels bioconda
        conda config --add channels conda-forge
        conda config --add channels gurobi
        
        # create conda environment and install phables
        conda create -n phables -c vijinim phables
        
        # activate environment
        conda activate phables
        ```
        
        Now you can go to [Setting up Gurobi](#setting-up-gurobi) to configure Gurobi.
        
        ### Option 2: Installing Phables from PyPi
        
        You can install Phables from PyPI at [https://pypi.org/project/phables/](https://pypi.org/project/phables/).
        
        ```bash
        pip install phables
        ```
        
        Now you can go to [Setting up Gurobi](#setting-up-gurobi) to configure Gurobi.
        
        ### Option 3: Downloading Phables from GitHub
        
        You can clone the Phables repository to your machine.
        
        ```bash
        git clone https://github.com/Vini2/phables.git
        ```
        
        Now go into the `phables` folder using the command
        
        ```bash
        cd phables/
        ```
        
        #### Using conda
        
        We recommend that you use [`conda`](https://docs.conda.io/en/latest/). Once you have installed `conda`, make sure you are in the `phables` folder. Now run the following commands to create a `conda` environment and activate it to run Phables.
        
        ```bash
        conda env create -f environment.yml
        conda activate phables
        ```
        
        #### Using pip
        
        If you prefer to use `pip` instead of `conda`, you can run the following command to install Phables using `pip`. Make sure you are in the `phables` folder.
        
        ```bash
        pip install .
        ```
        
        ### Setting up Gurobi
        
        The MFD implementation uses the linear programming solver [Gurobi](https://www.gurobi.com/). We chose Gurobi over open source solvers as Gurobi is fast and can solve large models (check the performance comparison at [https://www.gurobi.com/resources/open-source-linear-and-mixed-integer-programming-software-and-solvers/](https://www.gurobi.com/resources/open-source-linear-and-mixed-integer-programming-software-and-solvers/)).
        
        The `phables` conda environment and pip setup already include Gurobi. To handle large models without any model size limitations, you have to activate the (academic) license and add the key using the following command.
        
        ```bash
        grbgetkey <KEY>
        ```
        
        You can refer to further instructions at [https://www.gurobi.com/academia/academic-program-and-licenses/](https://www.gurobi.com/academia/academic-program-and-licenses/). Please note that this academic lisence is a file-based host-locked license, meaning that you can only run Gurobi on the machine that the license was obtained for. If you want to run on a cluster, you will have to contact your system admin and setup a floating network license. You can find more details at [https://support.gurobi.com/hc/en-us/articles/360013195412-How-do-I-obtain-a-free-academic-license-for-a-cluster-or-a-shared-computer-lab-](https://support.gurobi.com/hc/en-us/articles/360013195412-How-do-I-obtain-a-free-academic-license-for-a-cluster-or-a-shared-computer-lab-).
        
        ### Test the setup
        
        After setting up, run the following command to ensure that Phables is working.
        
        ```bash
        phables --help
        ```
        
        ## Example usage
        
        ```bash
        phables -g assembly_graph.gfa -p assembly_info.txt -hm edges.fasta.hmmout -ph phrog_annot.tsv -c coverage.tsv -b bam_files/ -o /output/path/
        ```
        
        Please refer to the [**documentation hosted at Read the Docs**](https://phables.readthedocs.io/en/latest/) for further information on how to obtain/format the inputs.
        
        ## Snakemake Pipeline
        
        To Do
        
        ## Reporting Issues
        
        Phables is still under testing. If you want to test (or break) Phables give it a try and report any issues and suggestions under [Phables Issues](https://github.com/Vini2/phables/issues).
        
        
        ## Acknowledgement
        
        Phables uses the Gurobi implementation of [MFD-ILP](https://github.com/algbio/MFD-ILP) and code snippets from [STRONG](https://github.com/chrisquince/STRONG), [METAMVGL](https://github.com/ZhangZhenmiao/METAMVGL), [GraphBin](https://github.com/metagentools/GraphBin) and [MetaCoAG](https://github.com/metagentools/MetaCoAG).
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
