Metadata-Version: 1.1
Name: puzzle
Version: 0.0.3
Summary: Web UI for searching genome variations
Home-page: https://github.com/robinandeer/puzzle
Author: Robin Andeer
Author-email: robin.andeer@gmail.com
License: MIT
Description: # Puzzle [![Build Status][travis-image]][travis-url] [![Test Coverage][coveralls-img]][coveralls-url]
        
        Variant Caller GUI and genetic disease analysis tool.
        
        ```bash
        $ git clone https://github.com/robinandeer/puzzle.git
        $ cd puzzle
        $ pip install --editable .
        $ puzzle view tests/fixtures/
        # open webbrowser on port 5000
        $ open http://localhost:5000
        ```
        
        ## Using Puzzle
        Puzzle will look for variant calling resources such as VCF files and [GEMINI][gemini] databases and visualize their content. It lets you inspect, annotate, and analyze variant calls.
        
        Puzzle is not primarily meant to be run as a persistant server but think of it more as an webinterface to quickly spin to visualize your variant calls.
        
        We set out to make `Puzzle` both very simple to install as well as intuitive to use. You can be up and running in minutes with minimal prerequisites.
        
        ## Developing Puzzle
        Puzzle is a Python Flask app with a command line interface. It can work with multiple backends using plugins; raw VCFs, GEMINI, MongoDB.
        
        Anyone can help make this project better - read [CONTRIBUTING](CONTRIBUTING.md) to get started!
        
        ### Install for development
        I decided to try out [Otto][otto] for this project so make sure you have it installed :smile:
        
        ```bash
        $ git clone https://github.com/robinandeer/puzzle.git
        $ cd puzzle
        $ otto dev
        $ otto dev ssh
        > npm install
        > sudo apt-get install vim python-pip git
        > pip install --user --editable .
        > puzzle /vagrant/tests/
        # open webbrowser on port 5000
        ```
        
        ## Testing Puzzle
        To run the tests, you need [pytest](pytest) installed in your system. You can install `pytest` together
        with the other development libraries by running `pip install -r requirements-dev.txt`.
        
        You will also need to download the database used for testing, which you can do by executing this command:
        
        ```
        wget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapFew.db -O tests/fixtures/HapMapFew.db
        ```
        
        Then, just run `py.test tests/`
        
        ## Use a gemini database ##
        
        Make sure you have gemini installed in your local environment
        
        ```
        puzzle --mode gemini view -i path/to/gemini_database.db
        ```
        
        ## Use ped info ##
        
        Puzzle uses the ped file to show more information in family view and in variant calls:
        
        ```
        puzzle view -i tests/fixtures/hapmap.vcf --family_file/-f tests/fixtures/hapmap.vcf
        ```
        
        ## Credits
        Puzzle Piece by Creative Stall from the Noun Project
        
        ## License
        MIT. See the [LICENSE](LICENSE) file for more details.
        
        
        [travis-url]: https://travis-ci.org/robinandeer/puzzle?branch=master
        [travis-image]: https://img.shields.io/travis/robinandeer/puzzle/master.svg?style=flat-square
        [coveralls-url]: https://coveralls.io/github/robinandeer/puzzle
        [coveralls-img]: https://img.shields.io/coveralls/robinandeer/puzzle.svg?style=flat-square
        [otto]: https://ottoproject.io/
        [gemini]: https://github.com/arq5x/gemini
        [pytest]: http://pytest.org/latest/
        
Keywords: p,u,z,z,l,e, ,d,e,v,e,l,o,p,m,e,n,t
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Environment :: Console
