template out other uses

_layouts/workflow-list.html

@@ -30,12 +30,11 @@ <h1 data-toc-skip>Workflows</h1>
                 <span tabindex="0" role="button" class="workflow show-when-galaxy-proxy-active" data-workflow="{{ workflow.trs_endpoint }}">Launch in Tutorial Mode</span>
 		<abbr class="hide-when-galaxy-proxy-active" title="This feature only available when the GTN is accessed through Galaxy">What is tutorial mode?</abbr>
                 <br/>
-                <a href="https://usegalaxy.eu/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-primary hide-when-galaxy-proxy-active">Import to UseGalaxy.eu</a>
-		<br/>
-                <a href="https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-primary hide-when-galaxy-proxy-active">Import to UseGalaxy.org</a>
-		<br/>
-                <a href="https://usegalaxy.org.au/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-primary hide-when-galaxy-proxy-active">Import to UseGalaxy.org.au</a>
-		<br/>
+		{% assign servers = site | list_usegalaxy_servers %}
+		{% for server in servers %}
+			<a href="{{ server.url }}/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-primary hide-when-galaxy-proxy-active">Import to {{ server.name }}</a>
+			<br/>
+		{% endfor %}
                 <a href="https://my.galaxy.training/?path=/workflows/trs_import%3Frun_form=true%26trs_url={{ workflow.trs_endpoint }}"
 		   class="btn btn-secondary hide-when-galaxy-proxy-active">Import to another server (≥23.0+ only!)</a>
             </td>

faqs/galaxy/support_admins.md

@@ -13,4 +13,5 @@ If you suspect there is something wrong with the server, or would like to reques
   - **Galaxy US:** [Email](mailto:[email protected]), [Gitter channel](https://gitter.im/galaxyproject/Lobby)
   - **Galaxy EU:** [Gitter channel](https://gitter.im/usegalaxy-eu/Lobby), [Request TIaaS](https://usegalaxy.eu/tiaas/)
   - **Galaxy AU:** [Email](mail:[email protected]), [Request a tool](https://request.usegalaxy.org.au/), [Request Data Quota](https://docs.google.com/forms/d/e/1FAIpQLSeiw6ajmkezLCwbXc3OFQEU3Ai9hGnBd967u9YbQ8ANPgvatA/viewform)
+  - **Galaxy FR:** [Request TIaaS](https://usegalaxy.fr/tiaas/)
   - Other Galaxy servers? Check the homepage for more information.

faqs/gtn/contributors_getting_started.md

@@ -15,7 +15,7 @@ Below is a checklist of things to look out for to help you get started. If you f
 Basic:
 
 - **Test** the tutorial on a running Galaxy instance
-   - For example [Galaxy Main](https://usegalaxy.org), [Galaxy Europe](https://usegalaxy.eu), or [Galaxy Australia](https://usegalaxy.org.au)
+   - For example {% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}
    - Report any issues you run into
 - **Language** editing
   - Fix spelling and grammar mistakes

faqs/gtn/contributors_tours.md

@@ -9,7 +9,7 @@ contributors: [shiltemann]
 Perhaps you've been asked to review an interactive tour, or maybe you just want to try one out. The easiest way to run an interactive tour is to use the [Tour builder](https://tailordev.fr/blog/2017/07/19/the-galaxy-tour-builder-extension/) browser extension.
 
 1. Install the Tour Builder extension to your browser ([Chrome Web Store](https://chrome.google.com/webstore/detail/galaxy-tour-builder/mdfbapknmcpnbmggahhaegehbbbmhmgg), [Firefox add-on](https://addons.mozilla.org/en-US/firefox/addon/galaxy-tour-builder/)).
-2. Navigate to a Galaxy instance supporting the tutorial. To find which Galaxy instances support each tutorial, please see the dropdown menu next to the tutorial on the training website. Using one of the usegalaxy.\* instances ([Galaxy Main](https://usegalaxy.org), [Galaxy Europe](https://usegalaxy.eu), or [Galaxy Australia](https://usegalaxy.org.au)
+2. Navigate to a Galaxy instance supporting the tutorial. To find which Galaxy instances support each tutorial, please see the dropdown menu next to the tutorial on the training website. Using one of the usegalaxy.\* instances ({% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %})
 ) is usually a good bet.
 3. Start the Tour Builder plugin by clicking on the icon in your browser menu bar
 4. Copy the contents of the `tour.yaml` file into the Tour builder editor window

topics/admin/tutorials/introduction/slides.html

@@ -33,8 +33,10 @@
 
 # Where can Galaxy run?
 
+{% assign servers = list_usegalaxy_servers_shuffle %}
+
 * Cloud (SaaS)
-  - A usegalaxy.* site [Main](https://usegalaxy.org) [Europe](https://usegalaxy.eu) [Australia](https://usegalaxy.org.au/)
+  - A usegalaxy.* site: {% for server in servers %}[{{ server.human }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}
   - [Public Galaxy Servers](https://galaxyproject.org/use)
   - [Amazon EC2 or MS Azure](https://launch.usegalaxy.org/)
   - Semi-private cloud (e.g.: [NeCTAR](https://nectar.org.au/), [Jetstream](http://jetstream-cloud.org/))

topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md

@@ -104,12 +104,13 @@ We will import the JSON files into Galaxy to query them directory, however the f
 >
 {: .comment}
 
+{% assign servers = list_usegalaxy_servers_shuffle %}
 
 > <hands-on-title>Loading SRA Aligned Read Format (SARF) Object Metadata URLs into Galaxy</hands-on-title>
 >
 >This step needs to be repeated at the beginning of an analysis to refresh the metadata to the latest daily version.
 >
-> 1. Go to your Galaxy instance of choice such as one of the [usegalaxy.org](https://usegalaxy.org/), [usegalaxy.eu](https://usegalaxy.eu), [usegalaxy.org.au](https://usegalaxy.org.au) or any other.
+> 1. Go to your Galaxy instance of choice such as one of the {% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %} or any other.
 >
 > 2. Create a new history
 >

topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.md

@@ -448,7 +448,7 @@ Now that we have downloaded this file we can go to a Galaxy instance and start p
 
 > <hands-on-title>Upload `SraRunInfo.csv` file into Galaxy</hands-on-title>
 >
-> 1. Go to your Galaxy instance of choice such as one of the [usegalaxy.org](https://usegalaxy.org/), [usegalaxy.eu](https://usegalaxy.eu), [usegalaxy.org.au](https://usegalaxy.org.au) or any other. (This tutorial uses usegalaxy.org).
+> 1. Go to your Galaxy instance of choice such as one of the [UseGalaxy.* instances](https://galaxyproject.org/usegalaxy/) or any other. (This tutorial uses usegalaxy.org).
 > 1. Click *Upload Data* button:
 > ![Data upload button](../../images/upload_button.png)
 > 1. In the dialog box that would appear click "*Choose local files*" button:

topics/introduction/tutorials/galaxy-intro-short/slides.html

@@ -101,7 +101,8 @@
 
 # Find a Galaxy server
 
-- **The Big Three**: Galaxy Main ([usegalaxy.org](https://usegalaxy.org)), Galaxy Europe ([usegalaxy.eu](https://usegalaxy.eu)), Galaxy Australia ([usegalaxy.org.au](https://usegalaxy.org.au))
+{% assign servers = list_usegalaxy_servers_shuffle %}
+- **UseGalaxy.\***: {% for server in servers %}{{ server.human }} ([{{ server.name }}]({{ server.url }})){% if forloop.last %}{% else %}, {% endif %}{% endfor %}
 
   .image-50[![usegalaxy.* servers]({{site.baseurl}}/shared/images/usegalaxy_servers.png)]
 

topics/introduction/tutorials/galaxy-intro-short/slides_CAT_ES.html

@@ -108,7 +108,8 @@
 
 # Encuentra un servidor Galaxy
 
-- ** Los tres grandes **: Galaxy Main ([usegalaxy.org](https://usegalaxy.org)), Galaxy Europe ([usegalaxy.eu](https://usegalaxy.eu)), Galaxy Australia ([usegalaxy.org.au](https://usegalaxy.org.au))
+{% assign servers = list_usegalaxy_servers_shuffle %}
+- ** Los tres grandes **: {% for server in servers %}{{ server.human }} ([{{ server.name }}]({{ server.url }})){% if forloop.last %}{% else %}, {% endif %}{% endfor %}
 
   .image-75[![usegalaxy.* servidores]({{site.baseurl}}/shared/images/usegalaxy_servers.png)]
 

topics/introduction/tutorials/galaxy-intro-short/tutorial.md

@@ -62,9 +62,7 @@ contributions:
 >   > <comment-title>Different Galaxy servers</comment-title>
 >   >  This is an image of Galaxy Australia, located at [usegalaxy.org.au](https://usegalaxy.org.au/)
 >   >
->   > The particular Galaxy server that you are using may look slightly different and have a different web address:
->   > - The main Galaxy server is [usegalaxy.org](https://usegalaxy.org/)
->   > - The European Galaxy server is [usegalaxy.eu](https://usegalaxy.eu/)
+>   > The particular Galaxy server that you are using may look slightly different and have a different web address.
 >   >
 >   > You can also find more possible Galaxy servers at the top of this tutorial in **Available on these Galaxies**
 >   {: .comment}

topics/introduction/tutorials/galaxy-reproduce/tutorial.md

@@ -40,12 +40,13 @@ For more background information about Galaxy, have a look into the Galaxy public
 
 # What does Galaxy look like?
 
-Many different Galaxy servers exist. Some are public, some are private, some focus on a specific topic and others like the usegalaxy.\* servers cover a broad range of tools. To reproduce published results it is highly recommended to use the same Galaxy server that was used in the original study. In the case that this was a private server that is not accessible to you, you might want to use one of the main Galaxy servers: [usegalaxy.org](https://usegalaxy.org), [usegalaxy.eu](https://usegalaxy.eu), [usegalaxy.org.au](https://usegalaxy.org.au). To learn more about the different Galaxy servers visit the [slides: options for using Galaxy]({{site.baseurl}}/topics/introduction/tutorials/options-for-using-galaxy/slides.html#1). The particular Galaxy server that you are using may look slightly different than the one shown in this training. Galaxy instance administrators can choose the exact version of Galaxy they would like to offer and can customize its look to some extent. The basic functionality will be rather similar across instances, so don’t worry! In this training we will use the European Galaxy server on which the original analysis was performed and shared.
+{% assign servers = list_usegalaxy_servers_shuffle %}
+Many different Galaxy servers exist. Some are public, some are private, some focus on a specific topic and others like the usegalaxy.\* servers cover a broad range of tools. To reproduce published results it is highly recommended to use the same Galaxy server that was used in the original study. In the case that this was a private server that is not accessible to you, you might want to use one of the main Galaxy servers: {% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}. To learn more about the different Galaxy servers visit the [slides: options for using Galaxy]({% link /topics/introduction/tutorials/options-for-using-galaxy/slides.html %}). The particular Galaxy server that you are using may look slightly different than the one shown in this training. Galaxy instance administrators can choose the exact version of Galaxy they would like to offer and can customize its look to some extent. The basic functionality will be rather similar across instances, so don’t worry! In this training we will use the European Galaxy server on which the original analysis was performed and shared.
 
 
 > <hands-on-title>Log in or register</hands-on-title>
 > 1. Open your favorite browser (Chrome/Chromium, Safari or Firefox, but not Internet Explorer/Edge!)
-> 2. Browse to the [Galaxy Europe instance](https://usegalaxy.eu/) (recommended) or to a Galaxy instance of your choosing
+> 2. Browse to the [Galaxy Europe instance](https://usegalaxy.eu/) or to a Galaxy instance of your choosing
 > 3. Choose *Login or Register* from the navigation bar at the top of the page
 > 4. If you have previously registered an account with this particular instance of Galaxy (user accounts are *not* shared between public servers!), proceed by logging in with your registered *public name*, or email address, and your password.
 >

topics/teaching/tutorials/setup-tiaas-for-training/tutorial.md

@@ -12,7 +12,7 @@ objectives:
   - Identify if it is appropriate
   - Interact with the service administrators to arrange for infrastructure
 key_points:
-  - Infrastructure is available for running Galaxy trainings for free from UseGalaxy.eu, UseGalaxy.org, and UseGalaxy.org.au
+  - Infrastructure is available for running Galaxy trainings for free from UseGalaxy.*
   - This can be easier than setting up a local Galaxy and may have more resources available
   - But have a backup plan
 contributors:

topics/teaching/tutorials/workshop-intro/slides.html

@@ -245,9 +245,10 @@
 
 - Training materials: https://training.galaxyproject.org
 - Galaxy (an instructor will tell you which Galaxy to use)
-  - Main: https://usegalaxy.org
-  - EU: https://usegalaxy.eu
-  - Australia: https://usegalaxy.org.au
+  {% assign servers = list_usegalaxy_servers_shuffle %}
+  {% for server in servers %}
+  - {{ server.name }} {{ server.url }}
+  {% endfor %}
   - [Other](https://galaxyproject.org/use/)
 - Register/log in
   - You may receive an e-mail with an activation link

topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.md

@@ -82,7 +82,9 @@ This is a Galaxy tutorial based on material from the [COMBINE R RNAseq workshop]
 
 ## Import data from URLs
 
-Read sequences are usually stored in compressed (gzipped) FASTQ files. Before the differential expression analysis can proceed, these reads must be aligned to the reference genome and counted into annotated genes. Mapping reads to the genome is a very important task, and many different aligners are available, such as HISAT2 ({% cite kim2015hisat %}), STAR ({% cite dobin2013star %}) and Subread ({% cite Liao2013 %}). Most mapping tasks require larger computers than an average laptop, so usually read mapping is done on a server in a linux-like environment, requiring some programming knowledge. However, Galaxy enables you to do this mapping without needing to know programming and if you don't have access to a server you can try to use one of the publically available Galaxies e.g. [usegalaxy.org](https://usegalaxy.org), [usegalaxy.eu](https://usegalaxy.eu), [usegalaxy.org.au](https://usegalaxy.org.au/).
+{% assign servers = list_usegalaxy_servers_shuffle %}
+
+Read sequences are usually stored in compressed (gzipped) FASTQ files. Before the differential expression analysis can proceed, these reads must be aligned to the reference genome and counted into annotated genes. Mapping reads to the genome is a very important task, and many different aligners are available, such as HISAT2 ({% cite kim2015hisat %}), STAR ({% cite dobin2013star %}) and Subread ({% cite Liao2013 %}). Most mapping tasks require larger computers than an average laptop, so usually read mapping is done on a server in a linux-like environment, requiring some programming knowledge. However, Galaxy enables you to do this mapping without needing to know programming and if you don't have access to a server you can try to use one of the publically available Galaxies e.g. {% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}.
 
 The raw reads used in this tutorial were obtained from SRA from the link in GEO for the the mouse mammary gland dataset (e.g `ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP045%2FSRP045534`). For the purpose of this tutorial we are going to be working with a small part of the FASTQ files. We are only going to be mapping 1000 reads from each sample to enable running through all the steps quickly. If working with your own data you would use the full data and some results for the full mouse dataset will be shown for comparison. The small FASTQ files are available in [Zenodo](https://zenodo.org/record/4249555) and the links to the FASTQ files are provided below.