Galaxy Server administration

Recently added tutorials, slides, FAQs, and events in the admin topic

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📚 Alternative Celery Deployment for Galaxy

By: Helena Rasche

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.

Published: 2024-11-07T14:55:31+00:00
Tags: admin, ansible

❓ Why isn't my history updating?

By: Helena Rasche

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?

Published: 2024-10-30T10:44:58+00:00
Tags: faqs, admin

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

By: Helena Rasche, Thanh Le Viet

Published: 2024-10-30T10:44:58+00:00
Tags: faqs, admin

🖼️ Galaxy Administrator Time Burden and Technology Usage

By: Vlad Visan

##Context

Published: 2024-07-10T18:44:14+00:00
Tags: admin, deploying, maintenance, survey

❓ Using data source tools with Pulsar

By: Martin Wolstencroft

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

Published: 2024-01-19T19:50:15+00:00
Tags: faqs, admin

❓ Updating from 22.01 to 23.0 with Ansible

By: Helena Rasche, Lucille Delisle

Published: 2023-11-01T17:37:12+00:00
Tags: faqs, admin

❓ Debugging Memory Leaks

By: Marius van den Beek, Helena Rasche

memray is a great memory profiler for debugging memory issues.

Published: 2023-09-22T09:44:14+00:00
Tags: faqs, admin

❓ Galaxy UI is slow

By: Nate Coraor

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

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

❓ Tool missing from Galaxy

By: Nate Coraor

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

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

❓ Debugging tool memory errors

By: Nate Coraor

Often the tool output contains one of:

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

❓ Debugging tool errors

By: Nate Coraor

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

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

❓ Blank page or no CSS/JavaScript

By: Nate Coraor

This generally means that serving of static content is broken:

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

❓ Database Issues

By: Nate Coraor

For slow queries, start with EXPLAIN ANALYZE

Published: 2023-05-11T13:25:10+00:00
Tags: faqs, admin

📚 Monitoring Galaxy and Pulsar with Sentry

By: Marius van den Beek

Overview

Published: 2023-04-19T12:33:06+00:00
Tags: admin, ansible, git-gat

❓ Mapping Jobs to Specific Storage By User

By: Helena Rasche, Björn Grüning, Nate Coraor

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:

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

❓ Failing all jobs from a specific user

By: Helena Rasche, Björn Grüning

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

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

❓ Library Permission Issues

By: Helena Rasche

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.

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

❓ Time to git commit

By: Helena Rasche

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

❓ Using Git With Ansible Vaults

By: Helena Rasche

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

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

❓ Opening a split screen in byobu

By: Helena Rasche

Opening a split screen in byobu

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

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

By: Helena Rasche

Published: 2023-04-16T09:02:56+00:00
Tags: faqs, admin

📚 Customizing the look of Galaxy

By: Laila Los

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

Published: 2023-04-16T09:02:56+00:00
Tags: admin, git-gat

📚 Customizing the look of Galaxy (Manual)

By: Laila Los

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

Published: 2023-04-16T09:02:56+00:00
Tags: admin

📚 Deploying a Beacon v1 in Galaxy

By: Helena Rasche

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

Published: 2023-04-16T09:02:56+00:00
Tags: admin, ga4gh, beacon, git-gat

📚 Server Maintenance: Cleanup, Backup, and Restoration

By: Helena Rasche, Lucille Delisle, Nate Coraor

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

Published: 2023-04-16T09:02:56+00:00
Tags: admin, ansible, deploying, git-gat

📚 Setting up Celery Workers for Galaxy

By: Mira Kuntz

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.

Published: 2023-04-16T09:02:56+00:00
Tags: admin, ansible, git-gat

📚 Reference Data with Data Managers

By: Simon Gladman, Enis Afgan

Overview

Published: 2023-03-17T11:29:55+00:00
Tags: admin

📚 Deploying Tailscale/Headscale for private mesh networking

By: Helena Rasche

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.

Published: 2022-09-21T14:40:57+00:00
Tags: admin, wireguard, networking

📚 Deploying Wireguard for private mesh networking

By: Helena Rasche

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.

Published: 2022-09-21T08:23:59+00:00
Tags: admin, wireguard, networking

❓ Galaxy Admin Training Path

By: Helena Rasche

Published: 2022-07-22T14:24:02+00:00
Tags: faqs, admin

🖼️ Galaxy and Celery

By: Mira Kuntz

Can you eat it?

Published: 2022-07-16T17:42:54+00:00
Tags: admin, ansible, git-gat

📚 How I learned to stop worrying and love the systemd

By: Helena Rasche

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.

Published: 2022-07-06T17:13:50+00:00
Tags: admin, ansible, systemd

❓ How many mules?

By: Helena Rasche, Saskia Hiltemann

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.

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

❓ Customising the welcome page

By: Helena Rasche

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

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

By: Helena Rasche

By this reference, YAML doesn’t really care:

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

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

By: Helena Rasche, Nicola Soranzo, Simon Gladman

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.

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

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

By: Helena Rasche

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

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

❓ Error: "skipping: no hosts matched"

By: Helena Rasche

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

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

❓ What if you forget `--diff`?

By: Helena Rasche

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.

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

❓ Define once, reference many times

By: Nate Coraor, Saskia Hiltemann

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

❓ Variable connection

By: Helena Rasche

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.

Published: 2022-06-07T12:09:49+00:00
Tags: faqs, admin

🎥 Recording of Performant Uploads with TUS

By: Helena Rasche

A 7M long recording is now available.

Published: 2022-03-11T00:00:00+00:00
Tags: admin

❓ How to read a Diff

By: Helena Rasche

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

Published: 2022-03-01T10:29:25+00:00
Tags: faqs, admin

📚 Performant Uploads with TUS

By: Marius van den Beek, Helena Rasche, Lucille Delisle

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.

Published: 2022-03-01T10:29:25+00:00
Tags: admin

🎥 Recording of Galaxy Installation with Ansible

By: Nate Coraor, Helena Rasche

A 2H50M long recording is now available.

Published: 2022-03-01T00:00:00+00:00
Tags: admin, ansible, deploying, git-gat

🎥 Recording of Use Apptainer containers for running Galaxy jobs

By: Simon Gladman

A 43M long recording is now available.

Published: 2021-06-28T00:00:00+00:00
Tags: admin, jobs, ansible, git-gat

🎥 Recording of Galaxy Tool Management with Ephemeris

By: Catherine Bromhead

A 17M long recording is now available.

Published: 2021-06-28T00:00:00+00:00
Tags: admin, tools, git-gat

🎥 Recording of Galaxy Tool Management with Ephemeris

By: Catherine Bromhead

A 27M long recording is now available.

Published: 2021-06-28T00:00:00+00:00
Tags: admin, tools, git-gat

🎥 Recording of Galaxy Installation with Ansible

By: Nate Coraor

A 2H47M long recording is now available.

Published: 2021-06-28T00:00:00+00:00
Tags: admin, ansible, deploying, git-gat

🎥 Recording of Running Jobs on Remote Resources with Pulsar

By: Simon Gladman

A 1H28M long recording is now available.

Published: 2021-06-28T00:00:00+00:00
Tags: admin, ansible, jobs, git-gat

📚 Enable upload via FTP

By: Lucille Delisle

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.

Published: 2021-06-18T13:52:44+00:00
Tags: admin, data, git-gat

📚 Upgrading Galaxy

By: Simon Gladman

Overview

Published: 2021-06-08T09:15:42+00:00
Tags: admin, ansible

❓ Got lost along the way?

By: Helena Rasche

Published: 2021-06-07T08:12:11+00:00
Tags: faqs, admin

❓ Install tools via the Admin UI

By: Saskia Hiltemann

Published: 2021-03-24T13:50:23+00:00
Tags: faqs, admin

❓ Running Ansible on your remote machine

By: Helena Rasche

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.

Published: 2021-03-24T13:50:23+00:00
Tags: faqs, admin

❓ Operating system compatibility

By: Helena Rasche

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.

Published: 2021-03-24T13:50:23+00:00
Tags: faqs, admin

📰 Galaxy Admin Training Success

By: Helena Rasche

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

Published: 2021-03-01T00:00:00+00:00
Tags: news, admin, gat, event, pandemic, remote-teaching

🎥 Recording of Use Apptainer containers for running Galaxy jobs

By: Helena Rasche

A 16M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, jobs, ansible, git-gat

🎥 Recording of Training Infrastructure as a Service (TIaaS)

By: Helena Rasche

A 24M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, training, jobs, git-gat

🎥 Recording of Upgrading Galaxy

By: Simon Gladman

A 36M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible

🎥 Recording of Mapping Jobs to Destinations using TPV

By: Helena Rasche

A 31M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, jobs, git-gat

🎥 Recording of Connecting Galaxy to a compute cluster

By: Helena Rasche

A 6M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, jobs, ansible, git-gat

🎥 Recording of Connecting Galaxy to a compute cluster

By: Helena Rasche

A 31M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, jobs, ansible, git-gat

🎥 Recording of Galaxy Tool Management with Ephemeris

By: Catherine Bromhead

A 47M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, tools, git-gat

🎥 Recording of Galaxy Interactive Tools

By: Anthony Bretaudeau

A 44M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, interactive-tools

🎥 Recording of Galaxy Monitoring with Telegraf and Grafana

By: Automated Text-to-Speech

A 2M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, monitoring, git-gat

🎥 Recording of Galaxy Monitoring with Telegraf and Grafana

A 73M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, monitoring, git-gat

🎥 Recording of Data Libraries

By: Saskia Hiltemann

A 22M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, storage, git-gat

🎥 Recording of Storage Management

By: Gianmauro Cuccuru

A 18M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, storage

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

By: Automated Text-to-Speech

A 4M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin

🎥 Recording of Galaxy Installation with Ansible

By: Helena Rasche

A 53M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, deploying, git-gat

🎥 Recording of Running Jobs on Remote Resources with Pulsar

By: Simon Gladman

A 14M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, jobs, git-gat

🎥 Recording of Running Jobs on Remote Resources with Pulsar

By: Simon Gladman

A 57M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, jobs, git-gat

🎥 Recording of Ansible

By: John Davis

A 5M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible

🎥 Recording of Ansible

By: Martin Čech

A 61M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible

🎥 Recording of Galaxy Monitoring with gxadmin

By: Automated Text-to-Speech

A 2M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, monitoring, ansible, git-gat

🎥 Recording of Reference Data with CVMFS

By: Automated Text-to-Speech

A 3M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, git-gat

🎥 Recording of Reference Data with CVMFS

By: Simon Gladman

A 23M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: admin, ansible, git-gat

📚 Mapping Jobs to Destinations using TPV

By: Nate Coraor, Björn Grüning, Nuwan Goonasekera, Mira Kuntz

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

Published: 2021-01-17T11:37:17+00:00
Tags: admin, jobs, git-gat

🖼️ Storage Management

By: Nate Coraor, Martin Čech, Helena Rasche, Saskia Hiltemann

Data Libraries

Published: 2021-01-14T08:41:22+00:00
Tags: admin, ansible, storage, git-gat

📚 Data Libraries

By: Helena Rasche, Saskia Hiltemann

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

Published: 2021-01-14T08:41:22+00:00
Tags: admin, ansible, storage, git-gat

📚 Use Apptainer containers for running Galaxy jobs

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

Published: 2021-01-08T14:43:22+00:00
Tags: admin, jobs, ansible, git-gat

📚 Reference Data with CVMFS without Ansible

By: Simon Gladman, Helena Rasche

Overview

Published: 2020-06-17T17:37:46+00:00
Tags: admin

🖼️ Galaxy Interactive Tools

By: Nate Coraor, Estelle Ancelet, Anthony Bretaudeau

History

Published: 2020-03-02T18:20:57+00:00
Tags: admin, ansible, interactive-tools

🖼️ Running Jobs on Remote Resources with Pulsar

What are heterogenous compute resources?

Published: 2020-02-28T19:24:42+00:00
Tags: admin, ansible, jobs, git-gat

📚 Galaxy Interactive Tools

By: Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau

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 and run until terminated by the user. One common example of such a tool is Jupyter Notebook. Galaxy Interactive Tools are similar in purpose to Galaxy Interactive Environments (GIEs), but are implemented in a significantly different manner. Most notably, instead of directly invoking containers on the Galaxy server, dedicated Docker node, or as a Docker Swarm service (as is done for GIEs), 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.

Published: 2020-02-27T15:21:14+00:00
Tags: admin, ansible, interactive-tools

📚 Training Infrastructure as a Service (TIaaS)

By: Helena Rasche, Saskia Hiltemann

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

Published: 2020-02-12T14:46:40+00:00
Tags: admin, ansible, training, jobs, git-gat

🖼️ Galaxy Installation with Ansible

By: Simon Gladman, Nate Coraor

Install PostgreSQL & Galaxy extensions

Published: 2020-02-04T13:39:23+00:00
Tags: admin, ansible, deploying, git-gat

📚 Automation with Jenkins

By: Helena Rasche

Overview

Published: 2019-08-06T13:56:16+00:00
Tags: admin, ansible, automation

📚 Galaxy Installation on Kubernetes

Galaxy Helm Chart

Published: 2019-07-02T18:24:39+00:00
Tags: admin, kubernetes

📚 Managing Galaxy on Kubernetes

Managing Galaxy on Kubernetes

Published: 2019-07-02T18:24:39+00:00
Tags: admin, kubernetes

🖼️ Galaxy Monitoring

By: Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

Manage Jobs

Published: 2019-04-26T16:41:13+00:00
Tags: admin

🖼️ Galaxy Monitoring with gxadmin

By: Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

Database Queries

Published: 2019-04-26T16:41:13+00:00
Tags: admin, monitoring, ansible, git-gat

🖼️ Reference Data with CVMFS

By: Daniel Blankenberg, Simon Gladman, Helena Rasche

Built in Data

Published: 2019-04-26T16:41:13+00:00
Tags: admin, ansible, git-gat

🖼️ Galaxy on the Cloud

By: Simon Gladman

All these Clouds

Published: 2019-01-31T19:06:48+00:00
Tags: admin

🖼️ Empathy

By: Helena Rasche, Saskia Hiltemann

Part of the Job

Published: 2019-01-31T16:14:13+00:00
Tags: admin

📚 Galaxy Monitoring with Reports

By: Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

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

Published: 2019-01-31T15:17:51+00:00
Tags: admin, ansible, monitoring, git-gat, broken

🖼️ Galaxy Monitoring with Telegraf and Grafana

By: Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

Telegraf, InfluxDB, and Grafana

Published: 2019-01-31T15:17:51+00:00
Tags: admin, ansible, monitoring, git-gat

📚 Galaxy Monitoring with Telegraf and Grafana

By: Helena Rasche

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.

Published: 2019-01-31T15:17:51+00:00
Tags: admin, ansible, monitoring, git-gat

🖼️ Server Maintenance: Cleanup, Backup, and Restoration

By: Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

Server Maintenance

Published: 2019-01-31T15:17:51+00:00
Tags: admin, ansible, deploying, git-gat

📚 External Authentication

By: Nate Coraor, Nicola Soranzo, Helena Rasche

Overview

Published: 2019-01-29T19:10:52+00:00
Tags: admin, authentication

📚 Galaxy Installation with Ansible

By: Helena Rasche, Nate Coraor, Simon Gladman

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.

Published: 2019-01-28T10:40:06+00:00
Tags: admin, ansible, deploying, git-gat

📚 Galaxy Monitoring with gxadmin

By: Helena Rasche

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.

Published: 2019-01-28T04:20:16+00:00
Tags: admin, monitoring, ansible, git-gat

🖼️ Storage Management

By: Nate Coraor, Martin Čech, Helena Rasche

Object Store Plugins

Published: 2019-01-28T04:12:36+00:00
Tags: admin, ansible, storage

📚 Distributed Object Storage

By: Nate Coraor, Helena Rasche, Gianmauro Cuccuru

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.

Published: 2019-01-28T04:12:36+00:00
Tags: admin, ansible, storage

🖼️ Reference Genomes in Galaxy

By: Daniel Blankenberg, Simon Gladman

Overview

Published: 2019-01-28T04:08:04+00:00
Tags: admin

🖼️ uWSGI

By: Nate Coraor, Simon Gladman

What is uWSGI?

Published: 2019-01-28T04:08:04+00:00
Tags: admin

🖼️ Galaxy Troubleshooting

By: Martin Čech, Nate Coraor

In system administration…

Published: 2019-01-28T04:08:04+00:00
Tags: admin

🖼️ Gearing towards production

Production server

Published: 2019-01-28T04:08:04+00:00
Tags: admin

🖼️ External Authentication

By: Martin Čech, Nicola Soranzo

Auth Mechanisms supported

Published: 2019-01-28T04:08:04+00:00
Tags: admin, authentication

🖼️ Controlling Galaxy with systemd or Supervisor

By: Nate Coraor, Helena Rasche

class: special

Published: 2019-01-28T04:08:04+00:00
Tags: admin

🖼️ Galactic Database

By: Martin Čech, Nicola Soranzo, Nate Coraor, Helena Rasche

Galactic Database

Published: 2019-01-28T04:08:04+00:00
Tags: admin

📚 Running Jobs on Remote Resources with Pulsar

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.

Published: 2019-01-28T04:02:36+00:00
Tags: admin, ansible, jobs, git-gat

🖼️ Galaxy Tool Management with Ephemeris

Galaxy tools

Published: 2019-01-27T22:09:32+00:00
Tags: admin, tools, git-gat

📚 Galaxy Tool Management with Ephemeris

By: Martin Čech, Helena Rasche, Nicola Soranzo

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.

Published: 2019-01-27T22:09:32+00:00
Tags: admin, tools, git-gat

📚 Reference Data with CVMFS

By: Simon Gladman, Helena Rasche

Published: 2019-01-27T16:50:26+00:00
Tags: admin, ansible, git-gat

🖼️ Terraform

By: Helena Rasche

Why Terraform

Published: 2018-10-27T07:51:23+00:00
Tags: admin, terraform, deploying, cloud

📚 Deploying a compute cluster in OpenStack via Terraform

By: Helena Rasche

Overview

Published: 2018-10-27T07:51:23+00:00
Tags: admin, terraform, deploying, cloud

🖼️ Ansible

By: Helena Rasche

Configuration Management

Published: 2018-10-27T07:51:23+00:00
Tags: admin, ansible

📚 Ansible

By: Helena Rasche, Saskia Hiltemann

Overview

Published: 2018-07-11T08:27:13+00:00
Tags: admin, ansible

🖼️ Connecting Galaxy to a compute cluster

By: Nate Coraor, Björn Grüning, Nicola Soranzo, Helena Rasche

Galaxy Job Configuration

Published: 2018-01-07T13:46:01+00:00
Tags: admin, jobs, ansible, git-gat

📚 Connecting Galaxy to a compute cluster

By: Nate Coraor, Björn Grüning, Helena Rasche

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

Published: 2018-01-07T13:46:01+00:00
Tags: admin, jobs, ansible, git-gat

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

By: Nate Coraor, Björn Grüning, Helena Rasche

Users

Published: 2018-01-07T13:28:18+00:00
Tags: admin

🖼️ Advanced customisation of a Galaxy instance

By: Björn Grüning, Helena Rasche, Martin Čech

Setup

Published: 2017-06-27T19:49:22+00:00
Tags: admin

🖼️ Galaxy from an administrator's point of view

By: Valentin Marcon, Nate Coraor, Björn Grüning, Helena Rasche

Published: 2017-06-12T08:10:40+00:00
Tags: admin

🖼️ Docker and Galaxy

By: Bérénice Batut, Björn Grüning

Preparing Admin Training VMs

Published: 2016-09-29T17:43:47+00:00
Tags: admin

📚 Galaxy Database schema

By: Hans-Rudolf Hotz, Björn Grüning

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.

Published: 2016-07-20T11:10:47+00:00
Tags: admin