Galaxy Server administration

Resources related to configuration and maintenance of Galaxy servers

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Material

Core

These are the core, foundational topics for the majority of administration in Galaxy.

Lesson Slides Hands-on Recordings
Ansible
ansible
    • Galaxy Installation with Ansible
    ansible deploying git-gat
    • Galaxy from an administrator's point of view

    Jobs & Scheduling

    Learn how to use DRMAA and other resources to schedule your jobs on clusters

    Lesson Slides Hands-on Recordings
    Connecting Galaxy to a compute cluster
    jobs ansible git-gat
    Galaxy and Celery
    Mapping Jobs to Destinations
    ansible jobs git-gat
    • Running Jobs on Remote Resources with Pulsar
    ansible jobs git-gat
    • Use Singularity containers for running Galaxy jobs
    jobs ansible git-gat

    • Data Management & Reference Data

    Manage data like a pro: tips on scaling to 1PB and more.

    Lesson Slides Hands-on Recordings
    Data Libraries
    ansible storage git-gat
    • Distributed Object Storage
    ansible storage
    Reference Data with CVMFS
    ansible git-gat
    • Reference Data with CVMFS without Ansible
    Reference Data with Data Managers

    Further Learning

    These topics will let you further expand your knowledge. They all build upon what you learned in the core topics, and many expect that you have a setup identical to the one started in the core trainings.

    Lesson Slides Hands-on Recordings
    Automation with Jenkins
    ansible automation
    Enable upload via FTP
    data git-gat
    External Authentication
    authentication
    Galaxy Interactive Tools
    ansible interactive-tools
    • Galaxy Tool Management with Ephemeris
    tools git-gat
    • How I learned to stop worrying and love the systemd
    ansible systemd
    Performant Uploads with TUS
    • Training Infrastructure as a Service (TIaaS)
    ansible training jobs git-gat

    • Running Galaxy on the Cloud

    If acronyms like EKS, EC2, GCP, ECS, K8S mean anything to you, then you've found where your home! Run Galaxy on someone else's computer with Cloud based tutorials

    Lesson Slides Hands-on Recordings
    Deploying Tailscale/Headscale for private mesh networking
    wireguard networking
    Deploying Wireguard for private mesh networking
    wireguard networking
    Galaxy on the Cloud
    Managing Galaxy on Kubernetes
    kubernetes
    Galaxy Installation on Kubernetes
    kubernetes
    Deploying a compute cluster in OpenStack via Terraform
    terraform deploying cloud

    Maintaining a Production Galaxy

    Deployed Galaxy? Now what? All of the knowledge you need to maintain it long term.

    Lesson Slides Hands-on Recordings
    Galaxy Troubleshooting
    Gearing towards production
    Server Maintenance and Backups
    Upgrading Galaxy
    ansible
    • User, Role, Group and Quota managment

    Monitoring

    Monitor Galaxy like UseGalaxy.eu, learn the ins and outs of monitoring

    Lesson Slides Hands-on Recordings
    Galaxy Monitoring
    Galaxy Monitoring with Reports
    ansible monitoring git-gat
    Galaxy Monitoring with Telegraf and Grafana
    ansible monitoring git-gat
    • Galaxy Monitoring with gxadmin
    monitoring ansible git-gat

    • Deprecated Tutorials

    Please do not run these. They are outdated and for historical, archival purposes only.

    Lesson Slides Hands-on Recordings
    uWSGI

    Other

    Assorted Tutorials

    Lesson Slides Hands-on Recordings
    Advanced customisation of a Galaxy instance
    Controlling Galaxy with systemd or Supervisor
    Docker and Galaxy
    Empathy
    Galactic Database
    Galaxy Database schema

    Frequently Asked Questions

    Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

    Maintainers

    This material is maintained by:

    orcid logoAvatarHelena Rascheorcid logoAvatarNate Coraororcid logoAvatarSimon Gladmanorcid logoAvatarBjörn GrüningAvatarMartin Čech

    For any question related to this topic and the content, you can contact them or visit our Gitter channel.

    Contributors

    This material was contributed to by:

    orcid logoAvatarJohn DavisAvatarPablo MorenoAvatarAbdulrahman Azaborcid logoAvatarAnthony BretaudeauAvatarAlex Mahmoudorcid logoAvatarNicola Soranzoorcid logoAvatarSaskia Hiltemannorcid logoAvatarHans-Rudolf HotzAvatarGildas Le Corguilléorcid logoAvatarJohn Chiltonorcid logoAvatarTorfinn Nomeorcid logoAvatarBérénice BatutAvatarMartin ČechAvatarMira KuntzAvatarNuwan Goonasekeraorcid logoAvatarNate Coraororcid logoAvatarGianmauro Cuccuruorcid logoAvatarDaniel BlankenbergAvatarDave B.orcid logoAvatarLucille DelisleAvatarValentin Marconorcid logoAvatarSimon Gladmanorcid logoAvatarBjörn Grüningorcid logoAvatarHelena RascheAvatarEnis AfganAvatarMarius van den BeekAvatarMatthias Bernt