Genotype

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

$ 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 file for more details.