Recently added tutorials, slides, FAQs, and events in the admin topic
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+00:00Have 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+00:00Published: 2024-10-30T10:44:58+00:00
##Context
Published: 2024-07-10T18:44:14+00:00Data source tools such as UCSC Main will fail if Pulsar is the default destination.
Published: 2024-01-19T19:50:15+00:00memray is a great memory profiler for debugging memory issues.
Published: 2023-09-22T09:44:14+00:00There is a great Tutorial from @mvdbeek which we recommend you follow.
Published: 2023-05-11T13:25:10+00:00First, restart Galaxy and watch the log for lines like:
Published: 2023-05-11T13:25:10+00:00Often the tool output contains one of:
Published: 2023-05-11T13:25:10+00:00Tool stdout/stderr is available in UI under “i” icon on history dataset
Published: 2023-05-11T13:25:10+00:00This generally means that serving of static content is broken:
Published: 2023-05-11T13:25:10+00:00For slow queries, start with EXPLAIN ANALYZE
Published: 2023-05-11T13:25:10+00:00Overview
Published: 2023-04-19T12:33:06+00:00It 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+00:00This command will let you quickly fail every job from the user ‘service-account’ (replace with your preferred user)
Published: 2023-04-16T09:02:56+00:00When 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+00:00When looking at git log to see what you changed, you cannot easily look into
Published: 2023-04-16T09:02:56+00:00Opening a split screen in byobu
Published: 2023-04-16T09:02:56+00:00Published: 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.
Published: 2023-04-16T09:02:56+00:00Customizing 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+00:00This tutorial will guide you through setting up a GA4GH Beacon!
Published: 2023-04-16T09:02:56+00:00Keeping 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+00:00Celery 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+00:00Tailscale 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+00:00In 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+00:00Can you eat it?
Published: 2022-07-16T17:42:54+00:00Many 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+00:00Start 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+00:00By this reference, YAML doesn’t really care:
Published: 2022-06-07T12:09:49+00:00You 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+00:00The bare role name is just simplified syntax for the roles, you could equally specifiy role:
There can be multiple reasons this happens, so we’ll step through all of them.
Published: 2022-06-07T12:09:49+00:00If 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+00:00When 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+00:00A 7M long recording is now available.
Published: 2022-03-11T00:00:00+00:00If you haven’t worked with diffs before, this can be something quite new or different.
Published: 2022-03-01T10:29:25+00:00Here 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+00:00A 2H50M long recording is now available.
Published: 2022-03-01T00:00:00+00:00A 43M long recording is now available.
Published: 2021-06-28T00:00:00+00:00A 17M long recording is now available.
Published: 2021-06-28T00:00:00+00:00A 27M long recording is now available.
Published: 2021-06-28T00:00:00+00:00A 2H47M long recording is now available.
Published: 2021-06-28T00:00:00+00:00A 1H28M long recording is now available.
Published: 2021-06-28T00:00:00+00:00This 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+00:00It 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+00:00These 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+00:00The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.
Published: 2021-03-01T00:00:00+00:00A 16M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 24M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 36M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 31M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 6M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 31M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 47M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 44M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 2M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 73M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 22M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 18M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 4M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 53M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 14M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 57M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 5M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 61M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 2M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 3M long recording is now available.
Published: 2021-02-15T00:00:00+00:00A 23M long recording is now available.
Published: 2021-02-15T00:00:00+00:00This 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+00:00Data Libraries
Published: 2021-01-14T08:41:22+00:00Data libraries are a great way to provide structured repositories of data to
Published: 2021-01-14T08:41:22+00:00In 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+00:00Overview
Published: 2020-06-17T17:37:46+00:00History
Published: 2020-03-02T18:20:57+00:00What are heterogenous compute resources?
Published: 2020-02-28T19:24:42+00:00Galaxy 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+00:00Galaxy 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+00:00Install PostgreSQL & Galaxy extensions
Published: 2020-02-04T13:39:23+00:00Overview
Published: 2019-08-06T13:56:16+00:00Galaxy Helm Chart
Published: 2019-07-02T18:24:39+00:00Managing Galaxy on Kubernetes
Published: 2019-07-02T18:24:39+00:00Database Queries
Published: 2019-04-26T16:41:13+00:00Built in Data
Published: 2019-04-26T16:41:13+00:00The 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+00:00Telegraf, InfluxDB, and Grafana
Published: 2019-01-31T15:17:51+00:00Monitoring 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+00:00Server Maintenance
Published: 2019-01-31T15:17:51+00:00This 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+00:00We 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+00:00Object Store Plugins
Published: 2019-01-28T04:12:36+00:00You 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+00:00In system administration…
Published: 2019-01-28T04:08:04+00:00Auth Mechanisms supported
Published: 2019-01-28T04:08:04+00:00class: special
Published: 2019-01-28T04:08:04+00:00Pulsar 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+00:00Galaxy tools
Published: 2019-01-27T22:09:32+00:00This 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+00:00Why Terraform
Published: 2018-10-27T07:51:23+00:00Overview
Published: 2018-10-27T07:51:23+00:00Galaxy Job Configuration
Published: 2018-01-07T13:46:01+00:00The 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+00:00Users
Published: 2018-01-07T13:28:18+00:00Setup
Published: 2017-06-27T19:49:22+00:00For 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