# Deploying the tools and workflows on a Galaxy instance

Given Ephemeris 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 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@galaxy.org with password admin to access everything.

More information on the use of Galaxy Docker containers can be found here.