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The sources of the openSNP website
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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 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)

Usage

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

redis-server

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

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.

Dependencies

For Fedora 19:

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