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 (slides) and tutorial (tutorial) buttons below.

Material

Core

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

Lesson Slides Hands-on Recordings
Galaxy from an administrator's point of view
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Ansible plain text tutorial
Galaxy Installation with Ansible plain text tutorial

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 plain text tutorial
Mapping Jobs to Destinations tutorial
Running Jobs on Remote Resources with Pulsar plain text tutorial
Use Singularity containers for running Galaxy jobs tutorial

Data Management & Reference Data

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

Lesson Slides Hands-on Recordings
Data Libraries plain text tutorial
Distributed Object Storage plain text tutorial
Reference Data with CVMFS plain text tutorial
Reference Data with CVMFS without Ansible
tutorial
Reference Genomes in Galaxy
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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 tutorial
Enable upload via FTP tutorial
External Authentication plain text tutorial
Galaxy Interactive Tools plain text tutorial
Galaxy Tool Management with Ephemeris plain text tutorial
Performant Uploads with TUS
tutorial
Training Infrastructure as a Service (TIaaS) tutorial

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
Galaxy on the Cloud
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Managing Galaxy on Kubernetes tutorial
Galaxy Installation on Kubernetes tutorial
Deploying a compute cluster in OpenStack via Terraform plain text tutorial

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
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Gearing towards production
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Server Maintenance and Backups
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Upgrading Galaxy tutorial
User, Role, Group and Quota managment
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Monitoring

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

Lesson Slides Hands-on Recordings
Galaxy Monitoring
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Galaxy Monitoring with gxadmin plain text tutorial
Galaxy Monitoring with Reports tutorial
Galaxy Monitoring with Telegraf and Grafana plain text tutorial

Deprecated Tutorials

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 They are outdated and for historical, archival purposes only.

Lesson Slides Hands-on Recordings
uWSGI
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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:

AvatarHelena Rasche AvatarNate Coraor AvatarSimon Gladman AvatarBjörn Grüning AvatarMartin 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:

AvatarValentin Marcon AvatarNate Coraor AvatarBjörn Grüning AvatarHelena Rasche AvatarMartin Čech AvatarSaskia Hiltemann AvatarGianmauro Cuccuru AvatarBérénice Batut AvatarLucille Delisle AvatarNicola Soranzo AvatarHans-Rudolf Hotz AvatarSimon Gladman AvatarAnthony Bretaudeau AvatarDaniel Blankenberg AvatarAbdulrahman Azab AvatarMarius van den Beek AvatarTorfinn Nome AvatarMatthias Bernt AvatarNuwan Goonasekera AvatarEnis Afgan AvatarAlex Mahmoud AvatarPablo Moreno AvatarJohn Davis