Metadata-Version: 1.1
Name: genotype
Version: 2.0.1
Summary: Taboo provides an automated pipipeline for comparinggenotypes from different assays.
Home-page: https://github.com/robinandeer/genotype
Author: Robin Andeer
Author-email: robin.andeer@scilifelab.se
License: MIT
Description: <p align="center">
          <a href="https://github.com/Clinical-Genomics/genotype">
            <img width="240px" height="180px" src="artwork/icon.png"/>
          </a>
        </p>
        
        # Genotype [![Documentation Status][readthedocs-img]][readthedocs-url] [![Build Status][travis-img]][travis-url]
        Manage SNP calling comparisons at Clinical Genomics. The package exposes a CLI and a bare bones web interface to visualize results stored in a SQLite database.
        
        ## Install
        
        ```bash
        $ conda install -c bioconda pysam pyyaml sqlalchemy flask
        $ pip install genotype==2.0.0-beta3
        ```
        
        ## Deploy to Amazon Elastic Beanstalk
        
        This guide uses the command line utility for Elastic Beanstalk (EB): `eb`.
        
        1. Create a new application by running `eb init` in the root of the repository.
        2. Create a new environment by running `eb create genotype`
        3. Configure environment variables in the AWS console under "Configuration/Software Configuration/" for the new environment.
            - `SQLALCHEMY_DATABASE_URI`: the connection URI for the database you are using
            - `GENOTYPE_NO_SAVE`: don't bother storing uploaded Excel books since EB doesn't provide persistent storage. Just set it to "yes".
        4. Install `genotype` locally and using the same connection URI run: `genotype --database [DB_URI] init <path to SNPs>`
        
        ## License
        MIT. See the [LICENSE](LICENSE) file for more details.
        
        
        
        [readthedocs-url]: https://readthedocs.org/projects/genotype/?badge=latest
        [readthedocs-img]: https://readthedocs.org/projects/genotype/badge/?version=latest
        
        [travis-url]: https://travis-ci.org/Clinical-Genomics/genotype
        [travis-img]: https://img.shields.io/travis/Clinical-Genomics/genotype.svg?style=flat
        
Keywords: genotype development
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
