# 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
- In your browser, open your Galaxy homepage
- Log in using the admin email, or register a new account with it if it is the first time you use it
- Go to User -> Preferences in the top menu bar, then click on Manage API key
- If there is no current API key available, click on
Create a new keyto generate it
- 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.
Declare following variables:
galaxy_instance='<link to galaxy_instance>' api_key='<API key>'
<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
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
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
email@example.com with password
admin to access everything.
More information on the use of Galaxy Docker containers can be found here.