Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
The sources of the openSNP website
Ruby HTML JavaScript CSS Shell

Merge pull request #185 from audy/remove-vegas

removed vegas from Gemfile for #184
latest commit f76fed4d37
@tsujigiri tsujigiri authored
Failed to load latest commit information.
app changed genome browser to hg38, fixes #170
bin Update Rails to 4.2.*
config 1st implementation ga4gh beacon
db workaround for setting up new db
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 added some style changes hound recommended
testdata Updated gems, changed some bootstrap-files.
tmp fixing tests and a little refactoring
.gitignore added local logfile to gitignore
.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…
.travis.yml Use OS' packaged hiredis
Capfile Further work on capistrano staging-evironment
Gemfile removed vegas from Gemfile for #184
Gemfile.lock updated bundler
Guardfile Add spring and guard
LICENSE.md Reintroduces license, somehow disappeared
Procfile Added Procfile for Foreman support
README.md added instructions for getting started and running tests
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.md

openSNP 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 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.

Something went wrong with that request. Please try again.