Galaxy Server administration

📅 2025 Galaxy Admin Training (Brno)

Martin Čech — 2025-09-03T10:13:19+00:00

The ins and outs of setting up your own production quality Galaxy server

📰 Survey about a week-long Galaxy Admin Training in Europe

2025-04-16T00:00:00+00:00

🚀 Survey about a week-long Galaxy Admin Training in Europe 🇪🇺

📚 Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD)

2025-03-24T08:45:40+00:00

📚 Pulsar usage on SURF Research Cloud

2024-12-18T14:49:11+00:00

Using Pulsar via the SURF Research Cloud (SRC) allows researchers to start Pulsar instances on-demand to expand their computational resources and even access GPUs to help and analyze their data in a secure environment following the General Data Protection Regulations (GDPR).

📚 Galaxy usage on SURF Research Cloud

2024-12-18T14:49:11+00:00

Using Galaxy via the SURF Research Cloud (SRC) allows researchers to start Galaxy instances on-demand and analyze their data in a secure environment following the General Data Protection Regulations (GDPR). The instance provides secure authentication, where users must have a SURF Research account prior to this tutorial, have set the SURF Research Access Management (SRAM) authentication method, and connect an SSH key to their accounts. In case you are not familiar with SRC and need help in setting up your accounts, please follow the instructions on the SURF Knowledge Base

📅 Galaxy at SURF Research Cloud workshop

Mirela Minkova — 2024-12-18T14:49:11+00:00

Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. **Registration**: To sign up for the event, please send an email to [Mirela Minkova](mailto:mirela.minkova@surf.nl?subject=Registering%20SRC%20Galaxy%20Workshop)

📚 Create a subdomain for your community on UseGalaxy.eu

2024-11-27T11:57:56+00:00

This tutorial covers how to set up a subdomain on usegalaxy.eu. We will take here the example of the earth system subdomain and follow the step one by one.

📚 Alternative Celery Deployment for Galaxy

2024-11-07T14:55:31+00:00

Celery is a new component to the Galaxy world (ca 2023) and is a distributed task queue that can be used to run tasks asynchronously. It isn’t mandatory, but you might find some features you expect to use to be missing without it.

❓ Why isn't my history updating?

2024-10-30T10:44:58+00:00

Have you ever experienced that you would submit a job but your history wouldn’t update? Maybe it doesn’t scroll or the datasets stay permanently grey even when you know they should be complete, until you refresh the webpage?

❓ How can I get my container requiring jobs to run in a container?

2024-10-30T10:44:58+00:00

📰 Galaxy Administrator Time Burden and Technology Usage

2024-07-22T00:00:00+00:00

Have you wondered how difficult Galaxy is to run? How much time people must spend to run Galaxy?

🖼️ Galaxy Administrator Time Burden and Technology Usage

2024-07-10T18:44:14+00:00

##Context

📅 2023 Galaxy Admin Training (Ghent)

Björn Grüning — 2024-05-23T14:04:44+00:00

The ins and outs of setting up your own production quality Galaxy server

📅 Admin Training @ GCC 2022: Online Training Day

Helena Rasche — 2024-05-23T14:04:44+00:00

Free, global, training day ahead of the Galaxy Community Conference 2022. This day is meant to get you up to speed with the basics, so that you can get the most out of the training sessions at the GCC2022 conference!

📰 🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!

2024-01-31T00:00:00+00:00

Hey Galaxy admins! Have you ever wanted to administer your own instance from

❓ Using data source tools with Pulsar

2024-01-19T19:50:15+00:00

Data source tools such as UCSC Main will fail if Pulsar is the default destination.

❓ Updating from 22.01 to 23.0 with Ansible

2023-11-01T17:37:12+00:00

❓ Debugging Memory Leaks

2023-09-22T09:44:14+00:00

memray is a great memory profiler for debugging memory issues.

❓ Galaxy UI is slow

2023-05-11T13:25:10+00:00

There is a great Tutorial from @mvdbeek which we recommend you follow.

❓ Tool missing from Galaxy

2023-05-11T13:25:10+00:00

First, restart Galaxy and watch the log for lines like:

❓ Debugging tool memory errors

2023-05-11T13:25:10+00:00

Often the tool output contains one of:

❓ Debugging tool errors

2023-05-11T13:25:10+00:00

Tool stdout/stderr is available in UI under “i” icon on history dataset

❓ Blank page or no CSS/JavaScript

2023-05-11T13:25:10+00:00

This generally means that serving of static content is broken:

❓ Database Issues

2023-05-11T13:25:10+00:00

For slow queries, start with EXPLAIN ANALYZE

📚 Monitoring Galaxy and Pulsar with Sentry

2023-04-19T12:33:06+00:00

Overview

❓ Mapping Jobs to Specific Storage By User

2023-04-16T09:02:56+00:00

It is possible to map your jobs to use specific storage backends based on user! If you have e.g. specific user groups that need their data stored separately from other users, for whatever political reasons, then in your dynamic destination you can do something like:

❓ Failing all jobs from a specific user

2023-04-16T09:02:56+00:00

This command will let you quickly fail every job from the user ‘service-account’ (replace with your preferred user)

❓ Library Permission Issues

2023-04-16T09:02:56+00:00

When running setup-data-libraries it imports the library with the permissions of the admin user, rather locked down to the account that handled the importing.

❓ Time to git commit

2023-04-16T09:02:56+00:00

❓ Using Git With Ansible Vaults

2023-04-16T09:02:56+00:00

When looking at git log to see what you changed, you cannot easily look into

❓ Opening a split screen in byobu

2023-04-16T09:02:56+00:00

Opening a split screen in byobu

❓ How do I see what variables are set for a host?

2023-04-16T09:02:56+00:00

📚 Customizing the look of Galaxy

2023-04-16T09:02:56+00:00

Customizing your Galaxy instance makes it more recognizable at a glance, and can help communicate its purpose to its users.

📚 Deploying a Beacon v1 in Galaxy

2023-04-16T09:02:56+00:00

This tutorial will guide you through setting up a GA4GH Beacon!

📚 Customizing the look of Galaxy (Manual)

2023-04-16T09:02:56+00:00

Customizing your Galaxy instance makes it more recognizable at a glance, and can help communicate its purpose to its users.

📚 Server Maintenance: Cleanup, Backup, and Restoration

2023-04-16T09:02:56+00:00

Keeping your Galaxy cleaned up is an important way to retain space, especially since for many groups that is the

📚 Setting up Celery Workers for Galaxy

2023-04-16T09:02:56+00:00

Celery is a distributed task queue written in Python that can spawn multiple workers and enables asynchronous task processing on multiple nodes. It supports scheduling, but focuses more on real-time operations.

🛤️ Admin Training Course

2023-04-13T15:51:25+00:00

Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway will guide you through all the steps required to setup your own Galaxy server with Ansible, configuring it, and making it production ready.

📚 Reference Data with Data Managers

2023-03-17T11:29:55+00:00

Overview

📚 Deploying Tailscale/Headscale for private mesh networking

2022-09-21T14:40:57+00:00

Tailscale makes secure networking easy, it really is like magic. If you’ve used wireguard before, you know it takes a bit to setup and some configuration if you need to do anything fancy.

📚 Deploying Wireguard for private mesh networking

2022-09-21T08:23:59+00:00

In this tutorial we will briefly cover what Wireguard is and how you can leverage it for your needs. This will not make you an expert on Wireguard but will give you the tools you need in order to setup a local Wireguard network.

❓ Galaxy Admin Training Path

2022-07-22T14:24:02+00:00

🖼️ Galaxy and Celery

2022-07-16T17:42:54+00:00

Can you eat it?

📚 How I learned to stop worrying and love the systemd

2022-07-06T17:13:50+00:00

Many linux sysadmins with years and years of experience bemoan systemd (“it’s infecting everything! Now it wants to mess with time? And DNS???”) and journalctl (“unix was supposed to be about files!”) and while those are fair complaints and make systemd and friends wildly more opaque than traditional SysV and logging to files, there are some benefits that can be obtained, and may be interesting even to the wise old admins. There is a lot of convenience in systemd that can make the tradeoffs worth it.

❓ How many mules?

2022-06-07T12:09:49+00:00

Start with 2 and add more as needed. If you notice that your jobs seem to inexplicably sit for a long time before being dispatched to the cluster, or after they have finished on the cluster, you may need additional handlers.

❓ Customising the welcome page

2022-06-07T12:09:49+00:00

❓ Is YAML sensitive to True/true/False/false

2022-06-07T12:09:49+00:00

By this reference, YAML doesn’t really care:

❓ How do I know what I can do with a role? What variables are available?

2022-06-07T12:09:49+00:00

You don’t. There is no standard way for reporting this, but well written roles by trusted authors (e.g. geerlingguy, galaxyproject) do it properly and write all of the variables in the README file of the repository. We try to pick sensible roles for you in this course, but, in real life it may not be that simple.

❓ What is the difference between the roles with `role:` prefix and without?

2022-06-07T12:09:49+00:00

The bare role name is just simplified syntax for the roles, you could equally specifiy role: every time but it’s only necessary if you want to set additional variables like become_user

❓ Error: "skipping: no hosts matched"

2022-06-07T12:09:49+00:00

There can be multiple reasons this happens, so we’ll step through all of them.

❓ What if you forget `--diff`?

2022-06-07T12:09:49+00:00

If you forget to use --diff, it is not easy to see what has changed. Some modules like the copy and template modules have a backup option. If you set this option, then it will keep a backup copy next to the destination file.

❓ Define once, reference many times

2022-06-07T12:09:49+00:00

❓ Variable connection

2022-06-07T12:09:49+00:00

When the playbook runs, as part of the setup, it collects any variables that are set. For a playbook affecting a group of hosts named my_hosts, it checks many different places for variables, including “group_vars/my_hosts.yml”. If there are variables there, they’re added to the collection of current variables. It also checks “group_vars/all.yml” (for the built-in host group all). There is a precedence order, but then these variables are available for roles and tasks to consume.

🎥 Recording of Performant Uploads with TUS

2022-03-11T00:00:00+00:00

A 7M long recording is now available.

❓ How to read a Diff

2022-03-01T10:29:25+00:00

If you haven’t worked with diffs before, this can be something quite new or different.

📚 Performant Uploads with TUS

2022-03-01T10:29:25+00:00

Here you’ll learn to setup TUS an open source resumable file upload server to process uploads for Galaxy. We use an external process here to offload the main Galaxy processes for more important work and not impact the entire system during periods of heavy uploading.

🎥 Recording of Galaxy Installation with Ansible

2022-03-01T00:00:00+00:00

A 2H50M long recording is now available.

🎥 Recording of Use Apptainer containers for running Galaxy jobs

2021-06-28T00:00:00+00:00

A 43M long recording is now available.

🎥 Recording of Running Jobs on Remote Resources with Pulsar

2021-06-28T00:00:00+00:00

A 1H28M long recording is now available.

🎥 Recording of Galaxy Installation with Ansible

2021-06-28T00:00:00+00:00

A 2H47M long recording is now available.

🎥 Recording of Galaxy Tool Management with Ephemeris

2021-06-28T00:00:00+00:00

A 17M long recording is now available.

🎥 Recording of Galaxy Tool Management with Ephemeris

2021-06-28T00:00:00+00:00

A 27M long recording is now available.

📚 Enable upload via FTP

2021-06-18T13:52:44+00:00

This tutorial will guide you to setup an File Transfer Protocol (FTP) server so galaxy users can use it to upload large files. Indeed, as written on the galaxy community hub, uploading data directly from the browser can be unreliable and cumbersome. FTP will allow users to monitor the upload status as well as resume interrupted transfers.

📚 Upgrading Galaxy

2021-06-08T09:15:42+00:00

Overview

❓ Got lost along the way?

2021-06-07T08:12:11+00:00

❓ Install tools via the Admin UI

2021-03-24T13:50:23+00:00

❓ Running Ansible on your remote machine

2021-03-24T13:50:23+00:00

It is possible to have ansible installed on the remote machine and run it there, not just from your local machine connecting to the remote machine.

❓ Operating system compatibility

2021-03-24T13:50:23+00:00

These Ansible roles and training materials were last tested on Centos 7 and Ubuntu 18.04, but will probably work on other RHEL and Debian variants.

📰 Galaxy Admin Training Success

2021-03-01T00:00:00+00:00

The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.

🎥 Recording of Training Infrastructure as a Service (TIaaS)

2021-02-15T00:00:00+00:00

A 24M long recording is now available.

🎥 Recording of Use Apptainer containers for running Galaxy jobs

2021-02-15T00:00:00+00:00

A 16M long recording is now available.

🎥 Recording of Mapping Jobs to Destinations using TPV

2021-02-15T00:00:00+00:00

A 31M long recording is now available.

🎥 Recording of Upgrading Galaxy

2021-02-15T00:00:00+00:00

A 36M long recording is now available.

🎥 Recording of Storage Management

2021-02-15T00:00:00+00:00

A 18M long recording is now available.

🎥 Recording of Galaxy Monitoring with gxadmin

2021-02-15T00:00:00+00:00

A 2M long recording is now available.

🎥 Recording of Connecting Galaxy to a compute cluster

2021-02-15T00:00:00+00:00

A 6M long recording is now available.

🎥 Recording of Connecting Galaxy to a compute cluster

2021-02-15T00:00:00+00:00

A 31M long recording is now available.

🎥 Recording of Running Jobs on Remote Resources with Pulsar

2021-02-15T00:00:00+00:00

A 14M long recording is now available.

🎥 Recording of Running Jobs on Remote Resources with Pulsar

2021-02-15T00:00:00+00:00

A 57M long recording is now available.

🎥 Recording of Data Libraries

2021-02-15T00:00:00+00:00

A 22M long recording is now available.

🎥 Recording of Galaxy Monitoring with Telegraf and Grafana

2021-02-15T00:00:00+00:00

A 2M long recording is now available.

🎥 Recording of Galaxy Monitoring with Telegraf and Grafana

2021-02-15T00:00:00+00:00

A 73M long recording is now available.

🎥 Recording of User, Role, Group, Quota, and Authentication managment

2021-02-15T00:00:00+00:00

A 4M long recording is now available.

🎥 Recording of Galaxy Installation with Ansible

2021-02-15T00:00:00+00:00

A 53M long recording is now available.

🎥 Recording of Galaxy Tool Management with Ephemeris

2021-02-15T00:00:00+00:00

A 47M long recording is now available.

🎥 Recording of Reference Data with CVMFS

2021-02-15T00:00:00+00:00

A 3M long recording is now available.

🎥 Recording of Reference Data with CVMFS

2021-02-15T00:00:00+00:00

A 23M long recording is now available.

🎥 Recording of Galaxy Interactive Tools

2021-02-15T00:00:00+00:00

A 44M long recording is now available.

🎥 Recording of Ansible

2021-02-15T00:00:00+00:00

A 5M long recording is now available.

🎥 Recording of Ansible

2021-02-15T00:00:00+00:00

A 61M long recording is now available.

📚 Mapping Jobs to Destinations using TPV

2021-01-17T11:37:17+00:00

This tutorial heavily builds on the Connecting Galaxy to a compute cluster and it’s expected you have completed this tutorial first.

🖼️ Storage Management

2021-01-14T08:41:22+00:00

Data Libraries

📚 Data Libraries

2021-01-14T08:41:22+00:00

Data libraries are a great way to provide structured repositories of data to

📚 Use Apptainer containers for running Galaxy jobs

2021-01-08T14:43:22+00:00

In this tutorial you will learn how to configure Galaxy to run jobs using Apptainer containers provided by the BioContainers community.

📚 Reference Data with CVMFS without Ansible

2020-06-17T17:37:46+00:00

Overview

🖼️ Galaxy Interactive Tools

2020-03-02T18:20:57+00:00

History

🖼️ Running Jobs on Remote Resources with Pulsar

2020-02-28T19:24:42+00:00

What are heterogenous compute resources?

📚 Galaxy Interactive Tools

2020-02-27T15:21:14+00:00

Galaxy Interactive Tools (GxITs) are a method to run containerized tools that are interactive in nature. Interactive Tools typically run a persistent service accessed on a specific port, until terminated by the user. One common example of such a tool is Jupyter Notebook. Galaxy Interactive Tools are submitted through Galaxy’s job management system and thus are scheduled the same as any other Galaxy tool - on a Slurm cluster, for instance. Galaxy Interactive Tools were introduced in Galaxy Release 19.09.

📚 Training Infrastructure as a Service (TIaaS)

2020-02-12T14:46:40+00:00

Galaxy is widely used for teaching. In order to facilitate instructors, the Galaxy Project has developed Training Infrastructure as a Service (TIaaS).

🖼️ Galaxy Installation with Ansible

2020-02-04T13:39:23+00:00

Install PostgreSQL & Galaxy extensions

📚 Automation with Jenkins

2019-08-06T13:56:16+00:00

Overview

📚 Galaxy Installation on Kubernetes

2019-07-02T18:24:39+00:00

Galaxy Helm Chart

📚 Managing Galaxy on Kubernetes

2019-07-02T18:24:39+00:00

Managing Galaxy on Kubernetes

🖼️ Galaxy Monitoring

2019-04-26T16:41:13+00:00

Manage Jobs

🖼️ Galaxy Monitoring with gxadmin

2019-04-26T16:41:13+00:00

Database Queries

🖼️ Reference Data with CVMFS

2019-04-26T16:41:13+00:00

Built in Data

🖼️ Galaxy on the Cloud

2019-01-31T19:06:48+00:00

All these Clouds

🖼️ Empathy

2019-01-31T16:14:13+00:00

Part of the Job

📚 Galaxy Monitoring with Reports

2019-01-31T15:17:51+00:00

The reports application gives some pre-configured analytics screens. These are very easy to setup and can help with debugging issues in Galaxy.

🖼️ Galaxy Monitoring with Telegraf and Grafana

2019-01-31T15:17:51+00:00

Telegraf, InfluxDB, and Grafana

📚 Galaxy Monitoring with Telegraf and Grafana

2019-01-31T15:17:51+00:00

Monitoring is an incredibly important part of server monitoring and maintenance. Being able to observe trends and identify hot spots by collecting metrics gives you a significant ability to respond to any issues that arise in production. Monitoring is quite easy to get started with, it can be as simple as writing a quick shell script in order to start collecting metrics.

🖼️ Server Maintenance: Cleanup, Backup, and Restoration

2019-01-31T15:17:51+00:00

Server Maintenance

📚 External Authentication

2019-01-29T19:10:52+00:00

Overview

📚 Galaxy Installation with Ansible

2019-01-28T10:40:06+00:00

This tutorial assumes you have some familiarity with Ansible and are comfortable with writing and running playbooks. If not, please consider following our Ansible Tutorial first.

📚 Galaxy Monitoring with gxadmin

2019-01-28T04:20:16+00:00

We will just briefly cover the features available in gxadmin, there are lots of queries that may or may not be useful for your Galaxy instance and you will have to read the documentation before using them.

🖼️ Storage Management

2019-01-28T04:12:36+00:00

Object Store Plugins

📚 Distributed Object Storage

2019-01-28T04:12:36+00:00

You may find that your Galaxy files directory has run out of space, but you don’t want to move all of the files from one filesystem to another. One solution to this problem is to use Galaxy’s hierarchical object store to add an additional file space for Galaxy.

🖼️ Galaxy Troubleshooting

2019-01-28T04:08:04+00:00

In system administration…

🖼️ Reference Genomes in Galaxy

2019-01-28T04:08:04+00:00

Overview

🖼️ Gearing towards production

2019-01-28T04:08:04+00:00

Production server

🖼️ uWSGI

2019-01-28T04:08:04+00:00

What is uWSGI?

🖼️ External Authentication

2019-01-28T04:08:04+00:00

Auth Mechanisms supported

🖼️ Controlling Galaxy with systemd or Supervisor

2019-01-28T04:08:04+00:00

class: special

🖼️ Galactic Database

2019-01-28T04:08:04+00:00

Galactic Database

📚 Running Jobs on Remote Resources with Pulsar

2019-01-28T04:02:36+00:00

Pulsar is the Galaxy Project’s remote job running system. It was written by John Chilton (@jmchilton) of the Galaxy Project. It is a python server application that can accept jobs from a Galaxy server, submit them to a local resource and then send the results back to the originating Galaxy server.

🖼️ Galaxy Tool Management with Ephemeris

2019-01-27T22:09:32+00:00

Galaxy tools

📚 Galaxy Tool Management with Ephemeris

2019-01-27T22:09:32+00:00

This tutorial will introduce you to one of Galaxy’s associated projects - Ephemeris. Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. It aims to help automate, and limit the quantity of manual actions admins have to do in order to maintain a Galaxy instance.

📚 Reference Data with CVMFS

2019-01-27T16:50:26+00:00

🖼️ Terraform

2018-10-27T07:51:23+00:00

Why Terraform

📚 Deploying a compute cluster in OpenStack via Terraform

2018-10-27T07:51:23+00:00

Overview

🖼️ Ansible

2018-10-27T07:51:23+00:00

Configuration Management

📚 Ansible

2018-07-11T08:27:13+00:00

Overview

🖼️ Connecting Galaxy to a compute cluster

2018-01-07T13:46:01+00:00

Galaxy Job Configuration

📚 Connecting Galaxy to a compute cluster

2018-01-07T13:46:01+00:00

The tools that are added to Galaxy can have a wide variance in the compute resources that they require and work efficiently on.

🖼️ User, Role, Group, Quota, and Authentication managment

2018-01-07T13:28:18+00:00

Users

🖼️ Advanced customisation of a Galaxy instance

2017-06-27T19:49:22+00:00

Setup

🖼️ Galaxy from an administrator's point of view

2017-06-12T08:10:40+00:00

🖼️ Docker and Galaxy

2016-09-29T17:43:47+00:00

Preparing Admin Training VMs

📚 Galaxy Database schema

2016-07-20T11:10:47+00:00

For the hands-on examples you need access to a Galaxy server and access to its PostgreSQL database. You can set-up this yourself, or use the Galaxy Docker Image provided by Björn Grüning (https://github.com/bgruening/docker-galaxy-stable). During this tutorial, we will work with the Galaxy Docker Image.