Genocrunch

A web-based platform for the analysis of metagenomic and metataxonomic data

Official web server: https://genocrunch.epfl.ch

Rights

• Copyright: All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Laboratory of Intestinal Immunology, 2016-2018
• License: GNU AGPL 3 (See LICENSE.txt for details)
• Authors: AR Rapin, FPA David, C Pattaroni, J Rougemont, BJ Marsland and NL Harris

Resources

• Git clone URL: https://c4science.ch/source/genocrunch-2.1.git
• Documentation: https://c4science.ch/source/genocrunch-2.1
• License: https://www.gnu.org/licenses/agpl-3.0.md
• Dockerfile: https://github.com/genocrunch/genocrunch_docker
• Docker image https://hub.docker.com/r/genocrunch/genocrunch_docker

Framework

Genocrunch uses the ruby on Rails framework with a PostgreSQL database.

Supported platforms

• Linux (tested on Ubuntu 16.04 LTS and CentOS 7)
• macOS (tested on 10.12 Sierra)

Browser support

• Mozilla Firefox tested on version 60.0.1 Quantum (Ubuntu 16.04 LTS/Windows 10/macOS 10.13)
• Microsoft Edge tested on version 42.17134 (Windows 10)
• Google Chrome tested on version 67.0.3396.79 (Ubuntu 16.04 LTS/Windows 10)
• Opera tested on version 53.0 (Ubuntu 16.04 LTS/Windows 10)
• Safari tested on version 11.1 (macOS 10.13)

Requirements

• Ruby version 2.3.1
• Rails version 5.0.0
• Python version >=2.7.0 <3.0.0
• R (tested with version 3.4.0)

Installation (Debian Linux and macOS)

Ruby, Rails and PostgreSQL

Debian Linux

Uninstall possible pre-installed versions of ruby:

$ sudo apt-get purge ruby

(Re-)install ruby and Rails using rbenv (see here).

Install PostgreSQL and start PostgreSQL server:

$ sudo apt-get install postgresql postgresql-contrib libpq-dev
$ sudo service postgresql start

macOS

Install ruby and Rails using homebrew and rbenv (see here).

Install PostgreSQL and start PostgreSQL server with homebrew:

$ brew install postgresql
$ brew services start postgresql

Python

Debian Linux

$ sudo apt-get install build-essential python-dev python-pip
$ pip install numpy

Check that python version is between 2.7.0 and 3.0.0:

$ python -V

macOS

If not done yet, install Homebrew:

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install python 2.7 with Homebrew:

$ brew install python

Check that python version is between 2.7.0 and 3.0.0:

$ python -V

R

Debian Linux

Add the R repository to /etc/apt/sources.list:

#/etc/apt/sources.list
...
deb http://cran.rstudio.com/bin/linux/ubuntu xenial/
...

$ sudo apt-get install r-base-core libnlopt-dev libcurl4-openssl-dev libxml2 libxml2-dev

Open the R environment and check the R version:

$ R
> R.version.string

macOS

Update XQuartz and Xcode if needed.

Download the R binary from CRAN at https://cran.r-project.org/bin/macosx. Click on the downloaded .pkg file and follow the instructions.

R dependencies

Install required R packages from CRAN and bioconductor:

$ sudo R
> install.packages(c("ineq", "rjson", "fpc", "multcomp", "FactoMineR", "colorspace", "vegan", "optparse", "gplots", "fossil", "coin", "SNFtool", "devtools"))
> source("https://bioconductor.org/biocLite.R")
> biocLite("sva")
> library(devtools)
> install_github("igraph/rigraph")
> q()

Genocrunch web application

Create a new rails project and add the Genocrunch files:

$ rails new genocrunch -d postgresql -B
$ git clone https://git@c4science.ch/source/genocrunch-2.1.git /tmp/genocrunch
$ rsync -r /tmp/genocrunch/ ./genocrunch
$ sudo rm -r /tmp/genocrunch
$ cd genocrunch \
  && cp gitignore.keep .gitignore \
  && cp config/config.yml.keep config/config.yml \
  && cp config/database.yml.keep config/database.yml \
  && cp config/initializers/devise.rb.keep config/initializers/devise.rb \
  && cp config/environments/development.rb.keep config/environments/development.rb \
  && cp config/environment_variables.rb.keep config/environment_variables.rb \
  && cp db/seeds.rb.keep db/seeds.rb \
  && cp public/app/TERMS_OF_SERVICE.txt.keep public/app/TERMS_OF_SERVICE.txt

Run the install.sh script (this is not essential for the application):

$ chmod 755 install.sh
$ ./install.sh
$ source ~/.bashrc  # or .bash_profile for macOS

The Genocrunch web app will store data files in users/:

$ mkdir users

Or, to store data in another location, use a simlink:

$ mkdir /path/to/your/custom/storage/location
$ ln -s /path/to/your/custom/storage/location users

Ruby libraries (gems)

Use the Gemefile to install required gems:

$ bundle install

Set application configuration variables

Set the application configuration variables in the config/config.yml file to fit the current installation needs. All variables are documented in the development section of the file.

Edit the devise secret key in config/environment_variables.rb.

Set genocrunch emails

Set the email details that will be used by Genocrunch to send information such as registration confirmation link or password recovery link to users. The following example would set Genocrunch to use an hypothetical gmail address (app_email@gmail.com) in development.

#config/initializers/devise.rb

Devise.setup do |config|
  ...
  config.mailer_sender = "app_email@gmail.com"
  ...

#config/environments/development.rb

Rails.application.configure do
  ...
  config.action_mailer.default_url_options = { :host => 'localhost:3000' }
  config.action_mailer.smtp_settings = {
    :address => "smtp.gmail.com",
    :port => 587,
    :domain => "mail.google.com",
    :user_name => "app_email@gmail.com",
    :password => "app_email_password",
    :authentication => :plain,
    :enable_starttls_auto => true
  }
  ...

Setup the PostgreSQL server

Create a new role and a new database (you can create different users and databases for development, test and/or production):

$ sudo su postgres  # for macOS, replace postgres by _postgres
$ psql
postgres=# CREATE ROLE myusername WITH LOGIN PASSWORD 'mypassword';
postgres=# CREATE DATABASE my_application_db_name OWNER myusername;
postgres=# \q
$ exit

Set the config/database.yml file: In development, test and/or production sections, set the database, username and password to fit the corresponding PostgreSQL database. Also make sure to uncomment host: localhost:

#config/database.yml

...
database: my_application_db_name
...
username: myusername
...
password: mypassword
...
host: localhost
...

Finally, ensure the md5 identification is set in /etc/postgresql/9.?/main/pg_hba.conf:

#/etc/postgresql/9.?/main/pg_hba.conf
...
host    all             all             0.0.0.0/0               md5
...

Restart the PostgreSQL service:

$ sudo /etc/init.d/postgresql restart

Initialize the database

Two default users will be created: guest and admin. The guest user is required to use the application without registering/signing-in. The admin user is optional. Setting the guest and admin passwords and emails can be done prior to seeding the database, by editing the db/seeds.rb file:

#db/seeds.rb

User.create!([{username: 'guest',
               role: 'guest',
               storage_quota: 0, # In bytes (0=illimited)
               email: 'guest@guestmailbox.com', # <- HERE
               confirmed_at: '2017-01-01 00:00:00.000000',
               password: 'guest_account_password'}, # <- HERE
              {username: 'admin',
               role: 'admin',
               storage_quota: 0, # In bytes (0=illimited)
               email: 'admin@adminmailbox.com', # <- HERE
               confirmed_at: '2017-01-01 00:00:00.000000',
               password: 'admin_account_password'}]) # <- AND THERE
...

Run the following commands to create and seed the database. Caution: This will erase previous database tables. Use it for installation, not update. For updates, use migrations or SQL queries.

$ rake db:schema:load
$ rake db:seed

Run the Rails server

$ rails server

You can now access the application in your browser at http://localhost:3000 on your machine and your.ip.address:3000 on your network.

By default, the server runs in development mode.

1. Start workers
2. Prefered way:

$ RAILS_ENV=development bin/delayed_job -n 2  start

OR

$ RAILS_ENV=development bin/delayed_job -n 2 restart

• Alternative way (not recommanded):

$ rake jobs:work

You can now create new jobs (run analysis). Read the documentation (http://localhost:3000/home/doc) for details.

Create a new version

Versions of installed R packages can be referenced in the version page (http://localhost:3000/versions). For this, run the get_version.py script:

$ get_version.py

This will create a .json file in the working directory with a name looking like version_2017-12-18_18:03:08.898906.json.

Sign in as admin and navigate to Infos>Versions Click on the New Version button and fill the form. In the JSON field, copy the json string contained in the .json file previously created using the get_version.py script. Finally, click on the Create Version button.

Terms of service

Terms of service can be edited in public/app/TERMS_OF_SERVICE.txt.

Usage

See Infos>Doc in the application web page (http://localhost:3000/home/doc).

Cleaning up data storage

Old jobs can be deleted using the rake cleanup task as following. The maximum age allowed for analyses is defined in the config/config.yml file uder the fields max_sandbox_job_age, for general analyses and max_job_age for analyses created by logged in users.

$ rake cleanup

This can be added as a periodic cron task to automate the cleanup process. Note that Examples will not be deleted by this process.

Running on Docker

See here.