openSNP

a repository to which users can upload their SNP-sets (and exome-VCFs) from 23andme, deCODEme, FamilyTreeDNA, AncestryDNA and IYG-format (for participants of EBI genotyping). On upload, SNPs are annotated using the PLoS and Mendeley-APIs to show users the newest scientific research results on their SNPs. Each SNP is also linked to the relevant page on SNPedia. SNPs are ranked according to how many results could be gathered for SNPedia, PLoS and Mendeley (in that order). Users can send each other private messages as well as comment on SNPs and Phenotypes.

Users can enter phenotypes to assist future research. Search is handled using postgres directly via pg_search.

RSS-feeds are provided for uploaded genotypes and new publications.

You can monitor the sidekiq-workers on localhost:3000/sidekiq (useful in killing leftover tasks)

To load all standard achievements into the database run

rake db:seed OR rake db:setup (which also sets up the entire db)

Getting Started

Install Dependencies

redis
hiredis
postgres

Setup Config

All configuration is done via environment variables. A file with a working environment for development can be found at .env.example. Simply copy it to .env to use it as is. The dotenv gem will pick it up and set the environment variables.

Copy config/database.yml.example to config/database.yml and adapt to your database setup.

Initialize Database

bundle exec rake db:setup

Run Tests

bundle exec rake

This runs RSpec tests as well as the legacy test/unit ones.

Usage

You need to have the following running to ensure that everything works:

redis-server

sidekiq -q preparse,2 -q parse,2 -q deletegenotype -q fitbit -q fixphenotypes -q frequency -q genomegov -q mailnewgenotype -q mendeley_details -q mendeley -q pgp -q plos_details -q plos -q zipfulldata -q snpedia -q zipgenotyping -C config/sidekiq.yml -e development

rails s(erver)

Note: "serverscript" starts all these in detached screen-sessions.

To see all rake-tasks:

rake -vT

Deployment

Deployment is handled via capistrano (thanks Helge!). The most important capistrano tasks:

cap deploy

deploys the newest version to production.

cap sidekiq:{start,stop,restart}

handles the Sidekiq workers. Has to be started on reboot!

Dependencies

For Fedora 19:

yum install postgresql postgresql-devel hiredis hiredis-devel libxslt-devel libxslt libxml2 libxml2-devel

Contribute

If you want to contribute to openSNP, you are more than welcome to do so:

We use the issue tracker at GitHub for everything that needs to be done. And there is the mailing list which we use for discuss running openSNP.org and other issues not directly related to the code-base.
Running rake notes may give you some hints about things that can be improved.
In order to help improving the overall code style, take a look into .rubocop_todo.yml. In order to learn what it is all about take a look at rubocop and specifically this section of the README to learn more about it.

cartersgenes/snpr