Metadata-Version: 1.1
Name: compath
Version: 0.1.2
Summary: A web application for exploring and comparing the overlaps across pathway resources
Home-page: https://github.com/ComPath/ComPath
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Description-Content-Type: UNKNOWN
Description: ComPath |build| |coverage| |docs| |zenodo|
        ==========================================
        An integrative and extensible web application for exploring, analyzing, and curating pathway databases. ComPath is publicly available at https://compath.scai.fraunhofer.de/.
        
        This package exposes the Bio2BEL pathway packages into a web application containing multiple built-in visualization and
        analytics tools allowing for their analysis and comparison. By default, this packages wraps the following default
        packages:
        
        - `Bio2BEL KEGG <https://github.com/bio2bel/kegg>`_
        - `Bio2BEL Reactome <https://github.com/bio2bel/reactome>`_
        - `Bio2BEL WikiPathways <https://github.com/bio2bel/wikipathways>`_
        - `Bio2BEL MSig <https://github.com/bio2bel/msig>`_
        
        New pathway/gene signatures resources can be added by forking the `ComPath Template Repository <https://github.com/compath/compath_template>`_.
        
        Citation
        --------
        If you use ComPath in your work, please cite [1]_:
        
        .. [1] Domingo-Fernández, D., *et al.* (2019). `ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases <https://doi.org/10.1038/s41540-018-0078-8>`_. *npj Syst Biol Appl.*, 5(1):3.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        ``compath`` can be installed easily from `PyPI <https://pypi.python.org/pypi/compath>`_ with the
        following code in your favorite terminal:
        
        .. code-block:: sh
        
            python3 -m pip install compath
        
        or from the latest code on `GitHub <https://github.com/compath/compath>`_ with:
        
        .. code-block:: sh
        
            python3 -m pip install git+https://github.com/bio2bel/compath.git@master
        
        Setup
        -----
        Easiest
        ~~~~~~~
        After installing ``compath``, run from the command line:
        
        .. code-block:: sh
        
            python3 -m compath populate
        
        This command populates all of the relevant Bio2BEL repositories for the default list, and if any optional ComPath
        repositories have been registered with entry points, will also populated.
        
        For Developers
        ~~~~~~~~~~~~~~
        If you just cloned the repo and installed it from the source code, you can run the sh script ``load_compath.sh`` by
        typing :code:`sh load_compath.sh` in your terminal. This script will first install all packages and later populate the
        database.
        
        If you have already installed the packages, but not loaded the data. First, load
        `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_ (see 'Mapping across gene/protein identifiers' section). Next, load all individual pathway database
        packages KEGG, Reactome, WikiPathways, and MSigDB  with :code:`python3 -m compath populate`. This command assumes that
        these packages are already installed in your Python environment. You can check the packages installed by running
        :code:`python3 -m compath ls` in your terminal. Alternatively, you can populate each package independently by running:
        :code:`python3 -m bio2bel_kegg populate`, :code:`python3 -m bio2bel_reactome populate`,
        :code:`python3 -m bio2bel_wikipathways populate`, or :code:`python3 -m bio2bel_msig populate`.
        
        Mapping across gene/protein identifiers
        ---------------------------------------
        In order to load the gene sets from default packages, ComPath assumes that `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_
        has been already installed and populated. This package is required to perform the mapping from multiple Protein/Gene identifiers to HGNC symbols. The following steps are needed to install Bio2BEL HGNC:
        
        1. :code:`python3 -m pip install bio2bel_hgnc`
        2. :code:`python3 -m bio2bel_hgnc populate`
        
        
        Running the Web Application
        ---------------------------
        The application can be run simply with
        
        .. code-block:: bash
        
            python3 -m compath web
        
        This command the Flask development server locally, by default on port 5000 (http://localhost:5000).
        
        
        Curation Interface
        ------------------
        Load mappings between pathways directly from the `ComPath Curation <https://github.com/compath/curation>`_ package.
        
        .. code-block:: sh
        
            python3 -m compath load_mappings --connection="sqlite:////data/bio2bel.db"
        
        Load hierarchical mappings from a pathway database already containing that information (e.g., Reactome).
        
        .. code-block:: sh
        
            python3 -m compath load_hierarchies --connection="sqlite:////data/bio2bel.db"
        
        
        Create a user.
        
        .. code-block:: sh
        
            python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_user  'email' 'password'
        
        Make user admin.
        
        .. code-block:: sh
        
            python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_admin 'email'
        
        Docker Instructions
        -------------------
        
        Deployment of ComPath with Docker
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1. Build the container with compath as a name.
        
        .. code-block:: sh
        
            docker build -t compath:0.0.1 .
        
        
        2. Create the data container in which the data will be located.
        
        .. code::
        
            docker create -v /data --name compath-data compath:0.0.1
        
        
        
        3. Run docker container and connect it with the data container
        
        .. code::
        
            docker run --name=compath --volumes-from compath-data --restart=always -d compath:0.0.1
        
        
        ``For admin purposes and deploying ComPath inside Fraunhofer you can also run the following command``
        
        .. code-block:: sh
        
            sh create_and_build_container.sh
        
        Load Data
        ~~~~~~~~~
        
        Loads the KEGG, Reactome, and WikiPathways modules into ComPath.
        
        .. code-block:: sh
        
            docker exec -t -it compath /opt/compath/src/bin/load_data.sh
        
        Restart Container
        ~~~~~~~~~~~~~~~~~
        
        Restarts the compath container
        
        .. code-block:: sh
        
            docker restart compath
        
        
        .. |build| image:: https://travis-ci.org/ComPath/ComPath.svg?branch=master
            :target: https://travis-ci.org/ComPath/ComPath
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/ComPath/ComPath/coverage.svg?branch=master
            :target: https://codecov.io/gh/ComPath/ComPath?branch=master
            :alt: Coverage Status
        
        .. |docs| image:: http://readthedocs.org/projects/compath/badge/?version=latest
            :target: https://compath.readthedocs.io/en/latest/
            :alt: Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/compath/compath/badges/gpa.svg
            :target: https://codeclimate.com/github/compath/compath
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/compath.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/compath.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/compath.svg
            :alt: MIT License
        
        .. |zenodo| image:: https://zenodo.org/badge/118578699.svg
            :target: https://zenodo.org/badge/latestdoi/118578699
        
Keywords: Pathways,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
