Venue: Monasterium PoortAckere, Oude Houtlei 56

City: Ghent

Country: Belgium

Postcode: 9000

Learning objectives:

• Add technical support for a tutorial
• Be able to download and use data managers to add a reference genome and its pre-calculated indices into the Galaxy reference data system
• Be able to get Galaxy to send jobs to a remote Pulsar server
• Be able to use an Ansible playbook to install different flavors of Galaxy for different purposes
• Be able to use the dynamic job runner to make arbitrary destination mappings
• Be aware of the security implications of Interactive Tools
• Be familiar with the basics of installing, configuring, and using Slurm
• Be familiar with wildcard SSL certificates and how to get them from Let's Encrypt
• Configure Galaxy and Pulsar to send errors to Sentry
• Configure Galaxy to use it to process uploads
• Configure and start Celery workers
• Configure your Galaxy to serve Interactive Tools using an Ansible Playbook
• Configure your Galaxy to use Apptainer and BioContainers for running jobs
• Configure your Galaxy to use these reference genomes and indices
• Create a tutorial from scratch
• Create hands-on
• Create several charts
• Deal with the dependencies
• Deploy a Beacon
• Extract a list of tools from a workflow
• Have a basic understanding of the Interactive Tools (GxIT/GIE) Proxy, its purpose, and configuration
• Have a strong understanding of Galaxy job destinations
• Have an understanding of Sentry
• Have an understanding of how Galaxy's Ansible roles are structured and interact with one another
• Have an understanding of the way in which Galaxy stores and uses reference data
• Have an understanding of what CVMFS is and how it works
• Have an understanding of what Celery is and how it works
• Have an understanding of what Pulsar is and how it works
• How to use the job resource parameter selection feature
• How to write a dynamic python function destination
• How to write a dynamic tool destination (DTD)
• Import data from disk
• Install Flower to the Galaxy venv and configure it
• Install Redis
• Install Sentry
• Install a role from Ansible Galaxy (repository unrelated to the Galaxy Project)
• Install and configure a Pulsar server on a remote linux machine
• Install and configure a RabbitMQ message queueing server
• Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
• Install these tools on a given Galaxy
• Interact with Galaxy via BioBlend.
• Join a training
• Know how to map tools to job destinations
• Learn Ansible basics
• Learn about Ephemeris
• Learn about different maintenance steps
• Learn about different options about Galaxy deployment.
• Learn about the Rule Based Uploader
• Learn gxadmin basics
• Learn the Galaxy user/group management and assign Quotas.
• Learn what a tool is and its structure
• Learn what to back up and how to recover
• Link a tutorial to a topic
• Make a tool ready for publishing in a ToolShed
• Make an educated decision about your preferred deployment model.
• Manage permissions
• Monitor a Celery task using the Flower dashboard
• Monitor performance with Sentry
• Request and manage trainings
• See some queries and learn how they help debug production issues
• Setup Grafana
• Setup InfluxDB
• Setup TIaaS
• Setup TUSd
• Setup Telegraf
• Setup a data library
• Setup and start the Galaxy reports app.
• Setup cleanups
• Setup postgres backups
• Start, run, and use an Interactive Tool
• The various ways in which tools can be mapped to destinations, both statically and dynamically
• Understand all components of the Galaxy job running stack
• Understand how the job conf controls Galaxy's jobs subsystem
• Understand the Role Based Access Control (RBAC) of Galaxy.
• Understand the job resource selector config and dynamic rule creation
• Understand the purpose and function of Galaxy job metrics
• Understand what Galaxy Interactive Tools are and how they work
• Use an Ansible playbook for all of the above
• Use an Ansible playbook for all of the above.
• Use the Planemo utilities to develop a tool
• Write a simple role
• Write functional tests

Organizer: Björn Grüning (https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/)

Host institutions: VIB

Event types:

• Workshops and courses

Sponsors: ELIXIR Europe

Scientific topics: Database management, Informatics, Data management