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        "author": "Robin Andeer",
        "author_email": "robin.andeer@gmail.com",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Topic :: Software Development"
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        "description": "# Puzzle [![Build Status][travis-image]][travis-url] [![Test Coverage][coveralls-img]][coveralls-url]\n\nDocumentation at www.robinandeer.com/puzzle/\n\nVariant Caller GUI and genetic disease analysis tool.\n\n```bash\n$ git clone https://github.com/robinandeer/puzzle.git\n$ cd puzzle\n$ pip install --editable .\n$ puzzle view tests/fixtures/\n# open webbrowser on port 5000\n$ open http://localhost:5000\n```\n\n## Using Puzzle\nPuzzle 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.\n\nPuzzle 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.\n\nWe 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.\n\n## Developing Puzzle\nPuzzle is a Python Flask app with a command line interface. It can work with multiple backends using plugins; raw VCFs, GEMINI, MongoDB.\n\nAnyone can help make this project better - read [CONTRIBUTING](CONTRIBUTING.md) to get started!\n\n### Install for development\nI decided to try out [Otto][otto] for this project so make sure you have it installed :smile:\n\n```bash\n$ git clone https://github.com/robinandeer/puzzle.git\n$ cd puzzle\n$ otto dev\n$ otto dev ssh\n> npm install\n> sudo apt-get install vim python-pip git\n> pip install --user --editable .\n> puzzle /vagrant/tests/\n# open webbrowser on port 5000\n```\n\n## Testing Puzzle\nTo run the tests, you need [pytest](pytest) installed in your system. You can install `pytest` together\nwith the other development libraries by running `pip install -r requirements-dev.txt`.\n\nYou will also need to download the database used for testing, which you can do by executing this command:\n\n```\nwget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapFew.db -O tests/fixtures/HapMapFew.db\n```\n\nTo test a gemini database with structural variants do:\n\n```\nwget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapSv.db -O tests/fixtures/HapMapSv.db\n```\n\nThen, just run `py.test tests/`\n\n## Use a gemini database\n\nMake sure you have gemini installed in your local environment\n\n```\npuzzle view path/to/gemini_database.db\n```\n\n## Use ped info ##\n\nPuzzle uses the ped file to show more information in family view and in variant calls:\n\n```\npuzzle view tests/fixtures/hapmap.vcf --family_file/-f tests/fixtures/hapmap.ped\n```\n\n## Establish a persistent local database\n\nPuzzle can establish a persistent local database, so you can keep work between sessions.\nThis enables other key features, such as gene lists for filtering and variant triage.\nFirst, you need to initialize a local database. Then one or more cases can be loaded and \nare then ready for viewing as soon as the web server is started.\n\n```\npuzzle init --root tests/fixtures\npuzzle load --root tests/fixtures tests/fixtures/hapmap.vcf\npuzzle view --root tests/fixtures\n```\n\n## Structural variant visualisation\n\nPuzzle enables visualisation also of structural variants with the use of '--variant-type sv' with '--load' or '--view'.\nEnjoy a list view of SVs as stored in gemini or vcf format. Key fields such as chromosomal band and size are enabled by default.\n\nIf gemini database with sv:s is downloaded, as described above, do:\n\n```\npuzzle view tests/fixtures/HapMapSv.db\n```\n\nTo view a example file with sv:s:\n\n```\npuzzle view tests/fixtures/hapmap.sv.vep.vcf.gz\n```\n\n## Build documentation\nDocumentation is generated using [Gitbook][gitbook]. Building the docs locally requires the GitBook CLI.\n\n```bash\n$ cd puzzle/\n$ npm install -g gitbook-cli\n$ gitbook serve ./docs\n```\n\nThe documentation can now be viewed on `http://localhost:4000/`.\n\n\n## Credits\nPuzzle Piece by Creative Stall from the Noun Project\n\n## License\nMIT. See the [LICENSE](LICENSE) file for more details.\n\n\n[travis-url]: https://travis-ci.org/robinandeer/puzzle?branch=master\n[travis-image]: https://img.shields.io/travis/robinandeer/puzzle/master.svg?style=flat-square\n[coveralls-url]: https://coveralls.io/github/robinandeer/puzzle\n[coveralls-img]: https://img.shields.io/coveralls/robinandeer/puzzle.svg?style=flat-square\n[otto]: https://ottoproject.io/\n[gemini]: https://github.com/arq5x/gemini\n[pytest]: http://pytest.org/latest/\n[gitbook]: https://www.gitbook.com/",
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