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The sources of the openSNP website
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app So that's why! deleted sass again, still one active admin file flying…
config Use lograge in production
db Reintroduces proper schema.rb
doc added rails skeleton
lib Remove even more last traces of Solr
public removing paths initializer
script Re-implement COPY approach in Ruby
spec Include all results in search feature test
test Include all results in search feature test
tmp fixing tests and a little refactoring
vendor/plugins use the dynamic_form gem instead of the plugin
.gitignore Include Snp creation in genotype parsing
.ruby-gemset Newest RVM uses .ruby-gemset instead of .rvmrc, also updated to 2.0.0…
.ruby-version Updates ruby to 2.1.2 with railsexpress patches. replaces debugger by…
.travis.yml Update Travis config
Capfile Further work on capistrano staging-evironment
Gemfile Use lograge in production
Gemfile.lock Updates Rails
Guardfile Add spring and guard
Procfile Added Procfile for Foreman support
README.rdoc Adds description of capistrano tasks to README for reference
Rakefile Run all the tests with rake test
Vagrantfile setting up capistrano
beautifier.rb Updated gems, changed some bootstrap-files. Fixes the sidekiq-CSS-issue in production
marshalled_snpedia_array Updates mediawiki gem. Fixes test by updating cassette.
serverscript Remove even more last traces of Solr
turnoffserver Updated gems, changed some bootstrap-files.


Build Status


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 implemented via the Solr-server.

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

Reminder: When new search-indexes are defined on models please run

rake sunspot:reindex

Reminder 2: You can monitor the sidekiq-workers on localhost:3000/sidekiq (useful in killing leftover tasks)

Reminder 3: To load all standard achievements into the database run

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


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


rake sunspot:solr:run OR rake sunspot:solr:start (runs in background)

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

cap deploy

deploys the newest version to production.

cap solr:{start,stop,restart}

handles the solr instance on production. Has to be started on reboot!

cap sidekiq:{start,stop,restart}

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

To do

Check the issues-page for things to fix/finish/do.


For Fedora 19:

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