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
# edit database.yml to point to your postgresql database
cp config/database.yml.example config/database.yml
cp config/app_config.yml.example config/app_config.yml
Generate Secret Token
bundle rake secret > secret_token
Initialize Database
bundle exec rake db:setup
Run Tests
bundle exec rake
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. Also, running rake notes may give you some hints about
things that can be improved.