Galaxy Installation with Ansible

Contributors

Authors: Simon Gladman Nate Coraor

Questions

• How does it all connect?

• What steps will we go through?

Objectives

• Get a high-level overview of a Galaxy server setup

Install PostgreSQL & Galaxy extensions

Speaker Notes

• The first step of a Galaxy deployment is the database.
• This is the foundation of everything.

Install Galaxy & Attach Storage

Speaker Notes

• Galaxy is deployed, and attached to the database.
• Next, Gunicorn is setup to run the Galaxy app.
• Storage is attached to Galaxy for storing data.
• And lastly compute is attached to Galaxy and the storage.

Configure NGINX

Speaker Notes

• Next, nginx is attached to UWSGI to proxy connections and speed up access.

Configure Job Handlers

Speaker Notes

• Job handlers are configured and deployed with the app.
• These connect to the compute and manage jobs.

Install & Configure Slurm

Speaker Notes

• Slurm is a much more intelligent resource manager than Galaxy.
• The job handlers are configured to connect to Slurm.
• Slurm deployment is explained in a separate tutorial.

Connect CVMFS & Reference Data

Speaker Notes

• CVMFS is deployed.
• Galaxy is configured to read data from CVMFS.
• Compute is configured to access it as well for jobs that need reference data.

Setup Remote Compute

Speaker Notes

• Lastly, we can scale Galaxy further with remote compute.
• Pulsar connected at a remote site will handle this.

Major Initial Decisions

• Where to install Galaxy
• Where to store Galaxy datasets
• Database location

Speaker Notes

• These are the major initial decisions you will face.
• Where to install Galaxy, what servers or VMs do you have available?
• Where to store the data?
• Do you have enough space for your users?
• Where to reliably store the database?

Where to install Galaxy

• Must be at same path on cluster - more on this in cluster sessions

Speaker Notes

• Galaxy should be installed somewhere that is available across the cluster.
• We’ll cover this in detail in the lesson.

Where to store Galaxy datasets

• Must be at same path on cluster
• Consider future scalability

Speaker Notes

• Where should data be stored?
• Do you have network-attached storage available?
• It must be available to the entire cluster where compute happens.

Database location

• Fast local, reliable storage
• Consider future scalability

Speaker Notes

• The database server should be very reliable.
• It does not need so much disk space, but consider future scalability.

Basic best practices

• Run as an unprivileged user
• When possible, separate code from data and configs
• Write protect code and configs

.left[All of these practices are supported in the galaxyproject.galaxy Ansible role and covered in the Galaxy Installation with Ansible tutorial!]

Speaker Notes

• Here are the basic best practices.
• Run without privileges so if someone gains access they are limited in what they can do.
• Ensure the code and configuration are separate.
• If someone manages to act as the galaxy user, this will prevent them from changing galaxy’s behaviour.
• All of these best practices are built into the ansible role.

Key Points

• Everything can be accomplished with Ansible roles from Galaxy
• You can easily deploy a base Galaxy, or one with more features.

Thank you!