Metadata-Version: 2.1
Name: biopax_explorer
Version: 1.2
Summary: A python library for BIOPAX manipulation
Home-page: https://forgemia.inra.fr/pegase/biopax-explorer
Author: FJR Moreews
Author-email: fjrmoreews@gmail.com
License: MIT
Description: # BIOPAX-Explorer 
        
        ## Features
        
        A python library for BIOPAX manipulation
        
        BIOPAX-Explorer is a Python package, designed to ease the manipulation of BIOPAX datasets.
        It exploits RDF and SPARQL, using a simple object-oriented, domain specific syntax.
        Biological Pathway Exchange (BioPAX) is a standard language
        that aims to enable integration, exchange, visualization and analysis of biological pathway data.
        BioPAX is defined in OWL  and is represented in the RDF/XML format.
        using these specifications and formats, BIOPAX-Explorer provides a 100 % compatible object-model
        with advanced query features, enabling quick analysis of datasets with a low learning curve. 
        
        ##### Documentation
        The Python code documentation is available on  [https://fjrmoreews.github.io/biopax-explorer/](https://fjrmoreews.github.io/biopax-explorer/)
         
        
        
        ##### Installation
        
        '
        pip install biopax-explorer
        '
        
        For large files, use a triple store , do not use the 'direct file in memory' option .
        the processing time can be long and a lot of RAM is needed. 
        
         
        
        
        
        ### Prerequisites
        
        The package relies mainly on rdfobj, RDFLib and  NetworkX.
        Optionnaly you can install  graph-tool for better performances on large graphs  [https://graph-tool.skewed.de/static/doc/quickstart.html](https://graph-tool.skewed.de/static/doc/quickstart.html).
        
        
        ### Source repository
        
        
        [git repository](https://forgemia.inra.fr/pegase/biopax-explorer)
        
        
        
        
        
        ### Docker installation
        
        #### ready to use Docker container
        
        We provide a easy to use Docker installation,tested with [Docker](https://www.docker.com/) on Linux and [Singularity](https://sylabs.io/)
        
        The  Biopax-Explorer Docker container is available at [https://hub.docker.com/r/fjrmore/biopax_explorer](https://hub.docker.com/r/fjrmore/biopax_explorer)
        
        The container can be used to deploy a jupyter enviroment with  tutorials and example notebooks
        
        A easy way to test Biopax Explorer is to use docker compose :
        
        ```
        # at the root of the repository
        docker-compose up
        #the triple store (fuseki) will be available on http://localhost:3030/  (login/password admin/admin)
        #Jupyter will be available on http://localhost:8888/  (password : pass)
        ```
        
        ```
        #contain of the docker-compose.yml file:
        
          biopax-explorer:
        
            image: fjrmore/biopax_explorer
        
            volumes:
              - ./script/:/work/script
              - ./input:/work/input
            
            links:
              - "db:tstore"
            ports:
              - "8888:8888"
            command: ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root","--NotebookApp.token='pass'" ]
        
        
          db:
        
            image: stain/jena-fuseki:4.0.0
         
            ports:
              - "3030:3030"
            volumes:
              - ./input/:/staging
              - ./db/fuseki:/fuseki
              - ./script/:/script
            environment: 
              - JVM_ARGS=-Xmx5024M
              - ADMIN_PASSWORD=admin
        
        
        ```
        
        
        ### Linux  and Mac installation (Ubuntu and Debian)
        
        ```
        pip install biopax-explorer
        
        ```
        
        
        ###  Windows installation
        
        
        Installation on windows is possible using at least 2 options :
        
        
        #### Installation on Windows using Docker-desktop
        This procedure has been tested on Windows 10 Enterprise.
        first install  Docker-desktop : see https://docs.docker.com/docker-for-windows/install/  
        
        when Docker-desktop is installed, open a power-shell terminal, then entre the followig commands:
        
        
        *  Biopax-Explorer in Python scripts
        
        ```
        $vol= (pwd).Path
        
        docker run -p 81:8888 -p 6006:6006 -it  -v ${vol}:/home/user fjrmore/Biopax-Explorer  python3 -c "import Biopax-Explorer; print('package p2g OK')"
        
        curl https://gitlab.inria.fr/fmoreews/Biopax-Explorer/-/raw/master/test/test.py -o test.py
        docker run -p 81:8888 -p 6006:6006 -it   -v ${vol}:/home/user fjrmore/Biopax-Explorer   python3 user/test.py
        
        ```
        
        ```
        #create your own script (mycript.py) , go in the directory where your script is located and execute it :.
        cd script_dir
        $vol= (pwd).Path
        docker run -p 81:8888 -p 6006:6006 -it   -v ${vol}:/home/user fjrmore/Biopax-Explorer  python3 mycript.py
        
        ```
        
        How to run power-shell : see [this link](https://www.digitalcitizen.life/ways-launch-powershell-windows-admin/)
        
        
         *  Biopax-Explorer in jupyter lab
        ```
        $vol= (pwd).Path
        docker run -p 81:8888 -p 6006:6006 -it   -v ${vol}:/home/user -e SHOW_PWD=true -e JUPYTER_PWD=password fjrmore/Biopax-Explorer  jupyter.sh
        ```
        
        then launch a browser and go to the following url : http://localhost:81/lab
        
        and enter the password (password)
        
        #### Installation on Windows using ubuntu terminal 
        
         See https://www.microsoft.com/en-us/p/ubuntu-2004-lts/9n6svws3rx71?activetab=pivot:overviewtab
        
        After you're environment configuration,
         follow the Docker or Conda + pip installation process (see above).
        
        
Platform: Posix; MacOS X;
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8.10
Description-Content-Type: text/markdown
Provides-Extra: testing
