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Installing openSNP

Hello and thanks so much for your interest in running our code! And maybe even contributing to the project. For more details on this see CONTRIBUTING.md

Table of Contents

How the site works

The site itself is based on Ruby on Rails (RoR). We usually try to use the newest version, but after major changes in a new version of RoR it may sometimes take a while for the switch to happen.

Setup

git is needed to download the newest sources:

git clone https://github.com/openSNP/snpr.git

Afterwards you'll have a new folder called "snpr" (it's not opensnp for historical reasons, the reason being startups ending with R were considered sexy back when) in which all the files reside.

Install Dependencies

Additionally, you may have to install a couple of development dependencies - libpq-dev and libsqlite3-dev. Depending on your operating system these are installed in different ways.

RVM

It's easier to use RVM to handle different Ruby versions, and the repository has all necessary files so that a new installation of RVM should find what it needs to download and install. There is an installation manual on the RVM homepage. After a successful installation and once you cd into the snpr/ directory, RVM should say something about installing the necessary Ruby version.

Otherwise, change into the cloned snpr directory and run the following commands to install necessary gems.

gem install bundler
bundle install

Setup config

All configuration is done via environment variables. Files for setting up working environments for testing and development are included (i.e. .env.test and .env.development). The dotenv gem will pick them up and set the environment variables. If you need to override variables locally, click here for instructions.

Copy config/database.yml.example to config/database.yml and adapt to your database setup. Specially, pay attention to the database username and password configuration. You may have to configure the postgres installation to provide necessary user privileges for creating the database.

Getting our Postgres database up and running

Install the Database

On a Linux Machine

Before the setup you need initialize the database. These steps have been tested on Fedora 25 but should be roughly the same for all other Linux distributions as well.

sudo postgresql-setup --initdb --unit postgresql

Add a user to postgres

sudo -u postgres createuser username

Get into the postgres console

sudo -u postgres psql postgres

Make your user a super user

ALTER USER username WITH SUPERUSER;

On MacOS

One of the easiest ways to get a Postgres installation is to use homebrew. Here's a handy step-by-step guide on how to get Homebrew and Postgres installed.

On Windows

Uh, we actually don't know that one yet. If you've done Postgres on Windows, please add to this section!

Setup the Database Tables

Before you can run openSNP you need to initialize the database tables that it will need. This can be done by running

bundle exec rake db:setup

After the setup the database is already for use. If you want login to the database and have a look you can use

psql snpr_development username

Running the server(s)

For development there's a small bash script called serverscript which starts the Rails server, the Redis server as well as the Sidekiq workers and Mailcatcher.

bash serverscript.sh

Voila! If everything worked out right so far, you should see openSNP portal at localhost:3000.

Additionally, there are many background tasks which live in app/workers, such as file parsing or talking to various APIs. They are handled by Sidekiq workers. You can monitor the sidekiq-workers on localhost:3000/sidekiq (useful in killing leftover tasks) once sidekiq is up and running.

In the development environment, the application will send the emails through Mailcatcher, which means all emails are just stored locally on your end and can easily be viewed at http://127.0.0.1:1080.

Talk to us

Please get in touch if you have trouble running openSNP on your end. You can send a mail to [email protected] if you want to discuss with us (or use the GH issues). There's also [email protected] if something broke on the webpage itself.

We're also available on Twitter:

@gedankenstuecke @helgerausch @philippbayer

There's also a Gitter where you can talk with us.

Last words

Thank you very much for your interest in the project and for the help of all volunteers who've helped us so far! There is a humans.txt where we celebrate all of you.

FAQs

  • I’m getting FATAL: Peer authentication failed for user "postgres"

    Please follow the suggestions here to configure your postgres installation. You will also need to grant CREATEDB privilege to the username in your database.yml.

  • I’m getting a weird error!

    Please open a new request on GitHub issue tracker.