COVID-19 analysis on usegalaxy.★

# Deploying the tools and workflows on a Galaxy instance

Given Ephemeris (opens new window) and the following files you can install all needed tools into any given Galaxy instance which you have admin access to.

# Install Ephemeris

Install Ephemeris using following command:

pip install ephemeris

# Download the necessary files

The workflows can be found in the galaxyproject/SARS-CoV-2 (opens new window) GitHub repository.

git clone https://github.com/galaxyproject/SARS-CoV-2.git

# Get the API key of an admin user on the galaxy instance of choice

Galaxy admin accounts are specified as a comma-separated email list in the admin_users directive of galaxy.yml.

  1. In your browser, open your Galaxy homepage
  2. Log in using the admin email, or register a new account with it if it is the first time you use it
  3. Go to User -> Preferences in the top menu bar, then click on Manage API key
  4. If there is no current API key available, click on Create a new key to generate it
  5. Copy your API key and keep it for later in this tutorial.

# Installing the tools and workflows

Go to the deploy directory of the recently cloned SARS-CoV-2 repository.

cd SARS-CoV-2/genomics/deploy

Declare following variables:

galaxy_instance='<link to galaxy_instance>'
api_key='<API key>'

Replace <link to galaxy_instance> with the link of the Galaxy instance the tools and workflows should be installed. <API key> need to be replaced by an Admin API key (see above).

Now it is time to install the tools and workflows using shed-tools install and workflow-install of the Ephemeris package.

shed-tools install -t all_covid_tools.yaml -g $galaxy_instance -a $api_key

workflow-install --publish_workflows --workflow_path workflows/ -g $galaxy_instance -a $api_key

# Docker

If you don't have access to any existing Galaxy instance, you can also use our preconfigured Docker image.

docker run --privileged -p 8080:80 quay.io/galaxy/covid-19-training

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to execute the COVID-19 analyses described on this page. The --privileged parameter is used to enable CVMFS, which makes the human reference genome hg38 available for the use of Minimap2. Login as admin using admin as username and password as password to access everything.

More information on the use of Galaxy Docker containers can be found here (opens new window).