One of the most important and recurring tasks for a Galaxy server admin is to keep the server up to date with security patches, minor fixes and major version upgrades.
Luckily for us, by using the best practice Ansible installation method that we have used throughout these tutorials, keeping our Galaxy server up to date is extremely easy.
We can get all the latest patches and fixes for our currently installed version of Galaxy by just re-running the Ansible playbook on a regular basis.
We can upgrade our Galaxy version by modifying the Ansible var files and re-running the playbook. It’s that simple.
This tutorial will show you how and discuss some of the things you need to keep in mind whenever you are updating or upgrading your Galaxy server.
Some notes on Galaxy versioning and releases.
As at June 2021, Galaxy has three new version releases per year - in each of January, May and September. The versions are denominated by the year and month - YY.MM. i.e. January 2021’s Galaxy release is version 21.01.
Each version also has an official branch in the GitHub repo named release_YY.MM. e.g. release_21.01
Galaxy versions will be supported with security fixes, bug patches and other improvements for one year from the time of release at which time they will become “End of Life” and will no longer be supported.
You have a VM or machine where you you have Galaxy installed.
You have completed at least the “Galaxy Installation with Ansible” tutorial.
You have command line and sudo access to the VM/computer where it is installed.
At the time of writing, the version of Galaxy that was installed with the “Galaxy Installation with Ansible” tutorial is 20.09. This tutorial is designed to upgrade the server to 21.01. If you already have a version equal to or higher than 21.01 running on your server, never fear! The process outlined below can still be used to upgrade to the latest version of Galaxy - just swap out 21.01 used below for the current latest version.
Find your current Galaxy server version
The first thing we will do in this tutorial is find the current installed version of the Galaxy. There are a few methods for determining this - You can find it in the GUI if you are an admin user or you can get it via the server API.
Once we know what our current version is, we can compare it with the latest available version
Hands-on: Get the current server version
Method 1: Via the Admin UI page
The currently installed version of Galaxy is shown on the Galaxy server’s Admin UI page.
Click on the Admin menu item to bring up the Admin UI.
The version of Galaxy currently running is displayed in the top left corner of the screen.
Figure 1: Screenshot of the Admin UI page showing the Galaxy server version.
Method 2: Via the API
In your browser - go to the following URL: https://galaxy.example.org/api/version (replacing galaxy.example.org with the hostname of your Galaxy server). The version will be displayed as follows:
Input: Bash
curl https://galaxy.example.org/api/version
Output: Browser window
{
"version_major": "20.09",
"extra": {}
}
Both methods above show the version of Galaxy that has been installed. At the time of writing, on this server it’s 20.09. Your version may differ depending on which version you installed initially.
Finding the latest release version
So, we have found out which version we are running on our server. But what is the current latest version of Galaxy that is available? There are quite a few ways of finding out.
Galaxy is released 3 times per year. If the time of year is around January/February, April/May or September/October there may be a new release about to be announced.
Probably the easiest way of finding the version number of the latest release is via the extensive Galaxy Documentation Website located at: https://docs.galaxyproject.org.
This site shows all of the release notes of all the available Galaxy versions and always has the latest release at the top of the list.
Figure 2: Screenshot of the Galaxy documentation webpage (https://docs.galaxyproject.org) showing the release versions. The latest version is at the top of the 'Releases' list.
We can see from this page that the latest release version of Galaxy is 21.01 (at the time of writing.)
Question: What is the current latest version?
As previously mentioned, the current latest release of Galaxy may not be 21.01. What version is the latest that you can see?
The importance of the release notes
Each release of Galaxy is accompanied by extensive release notes in two different “flavours.”
“Full release notes” which have extensive detail about all changes made since the last release. This version of the release notes is targetted to Administrators who may need to know about minor fixes, configuration details, security issues, new features and other things found in the latest version.
“User facing” release notes which provide an visual and interactive summary of the release highlights, additions and new features targetted towards end users, trainers and funders etc.
Before upgrading your Galaxy server to the latest version (or even a new version for that matter) - It is HIGHLY recommended that you read the release notes for that version. The notes are very extensive and may contain important information on any new features, links and how to configure them for your server.
Figure 3: An example selection from the release notes for Galaxy version 21.01 showing details on enhancements made with their associated Pull Requests in the GitHub repository.
Back up the Galaxy database
At the heart of every Galaxy server beats its database. The database is the most important part of the Galaxy server as it contains all of the metadata required for the server to operate and records details of all users, jobs, datasets etc since the server was started.
Sometimes new versions of Galaxy make changes to the database schema that require a database upgrade.
It is highly important that we back it up before making any substantial changes to the Galaxy server as things sometimes go wrong (inopportune power failures, disk crashes etc) and losing or corrupting the database is possible during an upgrade operation.
In a production environment it is really important to make regular backups of the database in any case. The usegalaxy.* servers all perform at least daily backups of their respective databases and even have replicate database servers just in case.
Hands-on: Back up the Galaxy database
We will be using the PostgreSQL pg_dump command to dump the complete contents of the Galaxy database to a file. From the usage text of the command:
pg_dump --help
pg_dump dumps a database as a text file or to other formats.
Usage:
pg_dump [OPTION]... [DBNAME]
We will use pg_dump and pipe its output through gzip to an output file to create a compressed text (SQL) representation of the database. We will need to do this as the galaxy user. It’s a good idea to create the backup file name with a sensible name and then copy it somewhere else like a cloud service.
-rw-rw-r-- 1 galaxy galaxy 94K Jun 8 04:12 galaxy_database_2009-1.sql.gz
As you can see, the database on our server isn’t currently huge though this will changes as your server gets more users, runs more jobs and stores more data. The current size for Galaxy Australia’s compressed database backup is ~11GB and growing.
Now that we have backed up our database we can move on to upgrading our Galaxy server to the latest version. For the sake of this tutorial, we will assume that the installed version is different to the latest version (at the time of writing - 20.09 vs 21.01). If that is not the case for you, then you can instead use this tutorial as a reference in the future.
Upgrading Galaxy to a new version
If you’ve been following best practices and using Ansible to install and configure your Galaxy server then you’re in luck - this step is going to be very easy! We just need to adjust the Galaxy version number in our group_vars/galaxyservers.yml file and re-run the playbook. If you haven’t been using Ansible then there are some notes on performing an upgrade located at: https://galaxyproject.org/admin/maintenance/. The Ansible method is much preferred and simple!
There are however a few things to consider before doing the actual upgrade, especially in a production environment.
Galaxy will be restarted.
Is this an appropriate time for that to happen?
Does it need to be scheduled with your users?
The database schema may change
Have you backed up the database?
Once you’ve made sure of these things, it’s time to do it!
Hands-on: Back up the Galaxy database
In this tutorial we will upgrade the server to version 21.01. This may be different for you. Please use the latest version instead.
Edit the group_vars/galaxyservers.yml file and change the galaxy_commit_id to the latest version. Use the form release_YY.MM or in this case release_21.01.
If you haven’t worked with diffs before, this can be something quite new or different.
If we have two files, let’s say a grocery list, in two files. We’ll call them ‘a’ and ‘b’.
Input: Old
$ cat old 🍎 🍐 🍊 🍋 🍒 🥑
Output: New
$ cat new 🍎 🍐 🍊 🍋 🍍 🥑
We can see that they have some different entries. We’ve removed 🍒 because they’re awful, and replaced them with an 🍍
Diff lets us compare these files
$ diff old new 5c5 < 🍒 --- > 🍍
Here we see that 🍒 is only in a, and 🍍 is only in b. But otherwise the files are identical.
There are a couple different formats to diffs, one is the ‘unified diff’
$ diff -U2 old new --- old 2022-02-16 14:06:19.697132568 +0100 +++ new 2022-02-16 14:06:36.340962616 +0100 @@ -3,4 +3,4 @@ 🍊 🍋 -🍒 +🍍 🥑
This is basically what you see in the training materials which gives you a lot of context about the changes:
--- old is the ‘old’ file in our view
+++ new is the ‘new’ file
@@ these lines tell us where the change occurs and how many lines are added or removed.
Lines starting with a - are removed from our ‘new’ file
Lines with a + have been added.
So when you go to apply these diffs to your files in the training:
Ignore the header
Remove lines starting with - from your file
Add lines starting with + to your file
The other lines (🍊/🍋 and 🥑) above just provide “context”, they help you know where a change belongs in a file, but should not be edited when you’re making the above change. Given the above diff, you would find a line with a 🍒, and replace it with a 🍍
Added & Removed Lines
Removals are very easy to spot, we just have removed lines
--- old 2022-02-16 14:06:19.697132568 +0100 +++ new 2022-02-16 14:10:14.370722802 +0100 @@ -4,3 +4,2 @@ 🍋 🍒 -🥑
And additions likewise are very easy, just add a new line, between the other lines in your file.
--- old 2022-02-16 14:06:19.697132568 +0100 +++ new 2022-02-16 14:11:11.422135393 +0100 @@ -1,3 +1,4 @@ 🍎 +🍍 🍐 🍊
Completely new files
Completely new files look a bit different, there the “old” file is /dev/null, the empty file in a Linux machine.
You should see in the Ansible output that Galaxy had to rebuild the client, update the database, rebuild its virtual environment and restart. If you weren’t using Ansible, these steps would all be manual and important not to get wrong. Ansible makes the entire process super simple for us.
Congratulations, you’re Galaxy server should now be updated to the latest version. You can check this by going to the Admin UI page or by using the API as described above.
Ongoing maintenance
The Galaxy development community continually support release versions of Galaxy for 1 year. They regularly update releases with bug fixes, patches and security enhancements. Therefore it is important that we as administrators keep our Galaxy servers up to date regardless of which release we are running.
The easiest way to do this is to regularly re-run the Ansible playbook. It will check with GitHub and grab any new changes to Galaxy since the last time you ran it and automatically keep everything up to date. The large usegalaxy.* servers all re-run the playbook on a regular schedule for this purpose.
Regular running of the playbook also encourages you and your team members to make changes to the Ansible scripts not the live system (as live changes will be overwritten). This leads to a much more robust and consistent production Galaxy server for your users.
Conclusion
This tutorial has shown you how to keep your Galaxy server up to date with the latest version painlessly and simply following current best practice. We hope you enjoyed this tutorial and got something out of it.
You've Finished the Tutorial
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Key points
Using Ansible to keep your server up to date is the best practice method
Always backup the database before you do an upgrade in case anything goes wrong
Re-run the playbook from time to time to keep your Galaxy server up to date with any minor changes and patches
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Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012
@misc{admin-upgrading,
author = "Simon Gladman",
title = "Upgrading Galaxy (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/upgrading/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
doi = {10.1371/journal.pcbi.1010752},
url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
year = 2023,
month = {jan},
publisher = {Public Library of Science ({PLoS})},
volume = {19},
number = {1},
pages = {e1010752},
author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
editor = {Francis Ouellette},
title = {Galaxy Training: A powerful framework for teaching!},
journal = {PLoS Comput Biol} Computational Biology}
}
Congratulations on successfully completing this tutorial!
You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.
Simon Gladman
Questions:
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