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wrote contributing, readme and humanstxt
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Bastian Greshake
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CONTRIBUTING.md
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CONTRIBUTING.md
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# Table of contents
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[How to contribute](#how-to-contribute)
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[How to submit changes](#how-to-submit-changes)
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[Testing](#testing)
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[What to work on](#what-to-work-on)
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[Request enhancements](#request-enhancements)
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[Talk to us](#talk-to-us)
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[How the site works](#how-the-site-works)
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[Setup](#setup)
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[Install Dependencies](#install-dependencies)
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[RVM](#rvm)
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[Setup Config](#setup-config)
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[Initialize Database](#initialize-database)
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[Running the server](#running-the-server)
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[Last words](#last-words)
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# How to contribute
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Thank you very much for your interest in helping openSNP! We're always happy to see new faces here. To make this a safe and inclusive space there is a [code of conduct for the project](https://github.com/gedankenstuecke/snpr/blob/master/CODE_OF_CONDUCT.md).
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## How to submit changes
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We accept [pull requests](https://help.github.com/articles/using-pull-requests/) via the [GitHub interface](https://github.com/gedankenstuecke/snpr/pull/new/master)!
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We are using rubocop and Travis-CI. After you have submitted the request, rubocop will complain about any style-breaks (and it always complains) while Travis-CI will run all tests in the background to see whether the pull request broke anything.
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## Testing
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Inside snpr/:
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```
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bundle exec rake
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```
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This runs RSpec tests as well as the **legacy** test/unit ones.
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## What to work on
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The [issues page](https://github.com/gedankenstuecke/snpr/issues) has several open issues, some of which are [marked as "easy-first-bugs"](https://github.com/gedankenstuecke/snpr/issues?q=is%3Aopen+is%3Aissue+label%3Aeasy-first-bugs). Some other things to work on:
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- Currently we have two different testing environments - the legacy ones in test/unit, and the RSpec tests. It would be great to have all tests inside RSpec.
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- There are many minor style-problems which live in .rubocop_todo.yml inside snpr/.
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## Request enhancements
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Open an issue on the [issues page](https://github.com/gedankenstuecke/snpr/issues), or send a mail to snpr-development@googlegroups.com so we can get the ball rolling!
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## Talk to us
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You can always open an issue for specific problems, or send a mail to snpr-development@googlegroups.com if you want to discuss something or if you have any questions or need help with something. There's also info@opensnp.org if something broke on the webpage itself.
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We're also available on Twitter:
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@gedankenstuecke
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@helgerausch
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@philippbayer
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Watch this space for a yet-to-be-created IRC channel.
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## Last words
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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](https://github.com/gedankenstuecke/snpr/blob/master/public/humans.txt) where we celebrate all of you.
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INSTALL.md
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INSTALL.md
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# Installing openSNP
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Hello and thanks so much for your interest in running our code! Maybe even to contribute to the project. For more details on this see [CONTRIBUTING.md](https://github.com/gedankenstuecke/snpr/blob/master/CONTRIBUTING.md)
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## How the site works
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The site itself is based on Ruby on Rails (RoR). We usually try to use the newest version, but after major changes in new version RoR it may sometimes take a while for the switch to happen.
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## Setup
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git is needed to download the newest sources:
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```
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git clone git@github.com:gedankenstuecke/snpr.git
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```
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Afterwards you'll have a new folder called "snpr" (it's not opensnp for historical reasons) in which all the files reside.
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## Install Dependencies
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- redis
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- hiredis
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- postgres
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Depending on your operating system these are installed in different ways.
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### RVM
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It's easier to use [RVM](https://rvm.io/) 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
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about installing the necessary Ruby version.
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## Setup Config
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All configuration is done via environment variables. A file with a
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working environment for development can be found at `.env.example`.
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Simply copy it to `.env` to use it as is. The
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[dotenv](https://github.com/bkeepers/dotenv) gem will pick it up
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and set the environment variables.
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Copy `config/database.yml.example` to `config/database.yml` and adapt to
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your database setup if needed (note: it's not needed on my Fedora machine, experience may vary).
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## Initialize Database
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```
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bundle exec rake db:setup
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```
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## Running the server
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For development there's a small bash script called `serverscript` which starts the Rails server, the Redis server as well as the Sidekiq workers.
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```
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bash serverscript.sh
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```
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There are many background tasks which live in app/workers, such as file parsing or talking to various APIs, which are handled by Sidekiq workers. You can monitor the sidekiq-workers on [localhost:3000/sidekiq](http://localhost:3000/sidekiq) (useful in killing leftover tasks) once sidekiq is up and running.
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## Last words
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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.
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README.md
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README.md
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# openSNP [](https://travis-ci.org/gedankenstuecke/snpr)
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a repository to which users can upload their SNP-sets (and exome-VCFs) from
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Hello! [openSNP.org](https://opensnp.org) is a repository to which users can upload their SNP-sets (and exome-VCFs) from
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23andme, deCODEme, FamilyTreeDNA, AncestryDNA and IYG-format (for participants
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of EBI genotyping). On upload, SNPs are annotated using the PLoS and
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Mendeley-APIs to show users the newest scientific research results on their
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@@ -9,108 +9,20 @@ according to how many results could be gathered for SNPedia, PLoS and Mendeley
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(in that order). Users can send each other private messages as well as comment
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on SNPs and Phenotypes.
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Users can enter phenotypes to assist future research. Search is handled using
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postgres directly via pg_search.
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## Installing openSNP
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Please see [INSTALL.md](https://github.com/gedankenstuecke/snpr/blob/master/INSTALL.md) for more detailed instructions on how to run and setup openSNP.
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RSS-feeds are provided for uploaded genotypes and new publications.
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## Contributing to openSNP
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You can monitor the sidekiq-workers on
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[localhost:3000/sidekiq](http://localhost:3000/sidekiq) (useful in killing
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leftover tasks)
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Please see [CONTRIBUTING.md](https://github.com/gedankenstuecke/snpr/blob/master/CONTRIBUTING.md) for more detailed instructions on how to contribute.
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To load all standard achievements into the database run
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## Getting in contact
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You can always open an issue for specific problems, or send a mail to snpr-development@googlegroups.com if you want to discuss something or if you have any questions or need help with something. There's also info@opensnp.org if something broke on the webpage itself.
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```
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rake db:seed OR rake db:setup (which also sets up the entire db)
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```
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We're also available on Twitter:
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# Getting Started
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@gedankenstuecke
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@helgerausch
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@philippbayer
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## Install Dependencies
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- redis
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- hiredis
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- postgres
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## Setup Config
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All configuration is done via environment variables. A file with a
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working environment for development can be found at `.env.example`.
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Simply copy it to `.env` to use it as is. The
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[dotenv](https://github.com/bkeepers/dotenv) gem will pick it up
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and set the environment variables.
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Copy `config/database.yml.example` to `config/database.yml` and adapt to
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your database setup.
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## Initialize Database
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```
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bundle exec rake db:setup
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```
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## Run Tests
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```
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bundle exec rake
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```
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This runs RSpec tests as well as the **legacy** test/unit ones.
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# Usage
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You need to have the following running to ensure that everything works:
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```
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redis-server
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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
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rails s(erver)
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```
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Note: "serverscript" starts all these in detached screen-sessions.
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To see all rake-tasks:
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```
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rake -vT
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```
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# Deployment
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Deployment is handled via capistrano (thanks Helge!). The most important capistrano tasks:
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```
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cap deploy
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```
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deploys the newest version to production.
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```
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cap sidekiq:{start,stop,restart}
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```
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handles the Sidekiq workers. Has to be started on reboot!
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# Dependencies
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For Fedora 19:
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```
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yum install postgresql postgresql-devel hiredis hiredis-devel libxslt-devel libxslt libxml2 libxml2-devel
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```
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# Contribute
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If you want to contribute to openSNP, you are more than welcome to do so:
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* There's a [code of conduct](https://github.com/gedankenstuecke/snpr/blob/master/CODE_OF_CONDUCT.md) which lines out how we intereact with each other.
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* We use [the issue tracker at GitHub](https://github.com/gedankenstuecke/snpr/issues)
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for everything that needs to be done. And there is the [mailing list](https://groups.google.com/forum/#!forum/snpr-development) which we use for discuss running openSNP.org and other issues not directly related to the code-base.
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* Running `rake notes` may give you some hints about things that can be
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improved.
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* In order to help improving the overall code style, take a look into
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`.rubocop_todo.yml`. In order to learn what it is all about take a
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look at [rubocop](https://github.com/bbatsov/rubocop) and specifically
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[this section of the README](https://github.com/bbatsov/rubocop#automatically-generated-configuration)
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to learn more about it.
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Watch this space for a yet-to-be-created IRC channel.
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71
public/humans.txt
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public/humans.txt
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# _____ _ _ _____
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# / ____| \ | | __ \
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# ___ _ __ ___ _ __ | (___ | \| | |__) |
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# / _ \| '_ \ / _ \ '_ \ \___ \| . ` | ___/
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# | (_) | |_) | __/ | | |____) | |\ | |
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# \___/| .__/ \___|_| |_|_____/|_| \_|_|
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# | |
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# |_|
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/* TEAM /*
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Philipp Bayer
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Contact: philippbay@gmail.com
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Site: philipp-bayer.net
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Twitter: @philippbayer
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Location: Perth, Australia
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Bastian Greshake
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Contact: bgreshake@gmail.com
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Site: ruleofthirds.de
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Twitter: @gedankenstuecke
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Location: Frankfurt, Germany
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Helge Rausch
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Contact: helge@rausch.io
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Twitter: @helgerausch
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Location: Berlin, Germany
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/* Contributors /*
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Calvyn82 (https://github.com/Calvyn82)
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djab (https://github.com/djab)
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Austin Davis-Richardson (https://github.com/audy)
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Stephanie Smith-Unna (https://github.com/Treblesteph)
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/* THANKS /*
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Fabian Zimmer (logo-designer!)
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Madeleine Ball
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John Wilbanks
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Julia Reda
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Lore Mroz
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Scott Chamberlain
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Caroline Brix
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Nikolay Kolev
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Marcel Salathe
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Emanuel Moura
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Thomas Landrain
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Philip Brechler
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Samantha Clark
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Beau Gunderson
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Thomas Schiewerling
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Rhonda Lea Kirk Fries
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Tom Hodder
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Niclas Deißler
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Niels Muenck
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Cathal Garvey
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Tristan
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Daniel Ford
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Ben Creasy
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Mark Atwood
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Albert Manson
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Divya Mistry
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Sergey
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Nick
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Brian Degger
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Malin
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Joerg Rings
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/* SITE /*
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Where: https://opensnp.org
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Last Update: 2016-02-07
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Standards: HTML5, CSS
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Components: Ruby on Rails, Bootstrap, jQuery
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