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The sources of the openSNP website
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app Put workers accessing user_snps on same queue
bin Update Rails to 4.2.*
config Put workers accessing user_snps on same queue
db Reintroduces proper schema.rb
doc added rails skeleton
lib Refactors Zipfulldata to Helge's recs. Deletes unneeded cleaning tasks.
public removing paths initializer
script Add Munin plugin for the parse queue length
spec Fix phenotype comments
test Merge pull request #144 from tsujigiri/rails4
testdata Updated gems, changed some bootstrap-files.
tmp fixing tests and a little refactoring
.gitignore Get rid of most of the deprecation warnings
.hound.yml Tell Hound where the Rubocop config is
.rspec Fix tests
.rubocop.yml Let Rubocop walk over it
.ruby-gemset Newest RVM uses .ruby-gemset instead of .rvmrc, also updated to 2.0.0…
.ruby-version Updates ruby version, adds newsletter (with correct subject this time :P
.travis.yml Use OS' packaged hiredis
Capfile Further work on capistrano staging-evironment
Gemfile Update gems, use regular rubyzip release again
Gemfile.lock Update gems
Guardfile Add spring and guard
LICENSE.md Reintroduces license, somehow disappeared
Procfile Added Procfile for Foreman support
README.rdoc Removes Solr from README
Rakefile Run all the tests with rake test
Vagrantfile setting up capistrano
beautifier.rb Updated gems, changed some bootstrap-files.
config.ru 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.

README.rdoc

Build Status

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)

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!

To do

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

Dependencies

For Fedora 19:

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