Add variables for usegalaxy.star servers

_layouts/workflow-list.html

@@ -48,9 +48,10 @@ <h6 class="card-subtitle mb-2 text-muted">
   </button>
   <div class="dropdown-menu">
 			<a href="{{ site.url }}{{ site.baseurl }}/{{ workflow.path }}" class="dropdown-item">Download Galaxy Workflow.ga</a>
-			<a href="https://usegalaxy.eu/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="dropdown-item hide-when-galaxy-proxy-active">UseGalaxy.eu</a>
-			<a href="https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="dropdown-item hide-when-galaxy-proxy-active">UseGalaxy.org</a>
-			<a href="https://usegalaxy.org.au/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="dropdown-item hide-when-galaxy-proxy-active">UseGalaxy.org.au</a>
+			{% assign servers = list_usegalaxy_servers_shuffle %}
+			{% for server in servers %}
+			<a href="{{ server.url }}/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="dropdown-item hide-when-galaxy-proxy-active">{{ server.human }}</a>
+			{% endfor %}
 			<a href="https://my.galaxy.training/?path=/workflows/trs_import%3Frun_form=true%26trs_url={{ workflow.trs_endpoint }}"
 			   class="dropdown-item hide-when-galaxy-proxy-active">Import to another server (≥23.0+ only!)</a>
   </div>

_plugins/gtn.rb

@@ -10,6 +10,7 @@
 require './_plugins/gtn/scholar'
 require './_plugins/gtn/supported'
 require './_plugins/gtn/toolshed'
+require './_plugins/gtn/usegalaxy'
 require './_plugins/jekyll-topic-filter'
 require 'time'
 
@@ -375,6 +376,14 @@ def get_version_number(page)
       Gtn::ModificationTimes.obtain_modification_count(page['path'])
     end
 
+    def list_usegalaxy_servers(site)
+      Gtn::Usegalaxy.servers.map{|x| x.transform_keys(&:to_s)}
+    end
+
+    def list_usegalaxy_servers_shuffle(site)
+      Gtn::Usegalaxy.servers.map{|x| x.transform_keys(&:to_s)}.shuffle
+    end
+
     def topic_name_from_page(page, site)
       if page.key? 'topic_name'
         site.data[page['topic_name']]['title']

_plugins/gtn/supported.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require './_plugins/gtn/usegalaxy'
 
 module Gtn
   # Handle tool support queries
@@ -21,11 +22,7 @@ def self.calculate(data, tool_list)
       if data.nil? || data.empty? || tool_list.empty? || tool_list.nil?
         return {
           'exact' => [],
-          'inexact' => [
-            { 'name' => 'UseGalaxy.eu', 'url' => 'https://usegalaxy.eu', 'usegalaxy' => true },
-            { 'name' => 'UseGalaxy.org', 'url' => 'https://usegalaxy.org', 'usegalaxy' => true },
-            { 'name' => 'UseGalaxy.org.au', 'url' => 'https://usegalaxy.org.au', 'usegalaxy' => true }
-          ],
+          'inexact' => Gtn::Usegalaxy.servers.map{|x| x['usegalaxy'] = true },
         }
       end
 

_plugins/gtn/usegalaxy.rb

@@ -0,0 +1,15 @@
+module Gtn
+  module Usegalaxy
+    @@SERVERS = [
+      { name: 'UseGalaxy.eu', url: 'https://usegalaxy.eu', id: 'eu', human: 'Galaxy Europe'},
+      { name: 'UseGalaxy.org', url: 'https://usegalaxy.org', id: 'us', human: 'Galaxy Main'},
+      { name: 'UseGalaxy.org.au', url: 'https://usegalaxy.org.au', id: 'au', human: 'Galaxy Australia'},
+      { name: 'UseGalaxy.fr', url: 'https://usegalaxy.fr', id: 'fr', human: 'Galaxy France'}
+    ]
+
+    def self.servers
+      @@SERVERS
+    end
+
+  end
+end

bin/workflow-test.rb

@@ -1,12 +1,16 @@
 #!/usr/bin/env ruby
 # frozen_string_literal: true
+require './_plugins/gtn/usegalaxy'
 
 require 'open3'
 require 'json'
 
-GALAXIES = {
-  eu: { url: 'https://usegalaxy.eu', key: ENV.fetch('GALAXY_EU_KEY', 'NONE') },
-}
+GALAXIES = Gtn::Usegalaxy.servers.select{|s| s[:id] == "eu"}.map do |server|
+  [
+    server[:id],
+    { url: server[:url], key: ENV.fetch("GALAXY_#{server[:id].upcase}_KEY", 'NONE') }
+  ]
+end.to_h
 
 def test_workflow(workflow_file, galaxy_id)
   directory = File.dirname(workflow_file)

bin/workflows-fetch.rb

@@ -3,6 +3,8 @@
 require 'net/http'
 require 'uri'
 require 'yaml'
+require './_plugins/gtn/usegalaxy'
+
 
 def request(url)
   uri = URI.parse(url)
@@ -86,13 +88,11 @@ def fetch_workflowhub()
 
 
 # Parse the response
-workflows_eu = fetch_workflows('https://usegalaxy.eu')
-puts "INFO: Fetched #{workflows_eu.length} workflows from EU"
-workflows_org = fetch_workflows("https://usegalaxy.org")
-puts "INFO: Fetched #{workflows_org.length} workflows from ORG"
-workflows_aus = fetch_workflows("https://usegalaxy.org.au")
-puts "INFO: Fetched #{workflows_aus.length} workflows from AUS"
-workflows = workflows_eu + workflows_org + workflows_aus
+workflows = Gtn::Usegalaxy.servers.map {|server|
+  workflows = fetch_workflows(server[:url])
+  puts "INFO: Fetched #{workflows.length} workflows from #{server[:name]}"
+  workflows
+}.flatten
 
 # Cleanup the list
 workflows.filter! do |w|

faqs/galaxy/account_create.md

@@ -9,7 +9,11 @@ contributors: [jennaj, bernandez, samanthaanjei, wm75]
 
 1. To create an account at any public Galaxy instance, choose your server from the available [list of Galaxy Platforms](https://galaxyproject.org/use/).
 
-    There are 3 main public Galaxy servers: [UseGalaxy.org](https://usegalaxy.org/) (**US**), [UseGalaxy.eu](https://usegalaxy.eu/) (**EU**), and [UseGalaxy.org.au](https://usegalaxy.org.au/) (**AU**).
+    There are several UseGalaxy servers:
+    {% assign servers = nil | list_usegalaxy_servers_shuffle %}
+    {% for server in servers %}
+    - [{{ server.name }}]({{ server.url }}) (**{{ server.id | upcase }}**)
+    {% endfor %}
 
 2. Click on **"Login or Register"** in the masthead on the server.
 

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

short/galaxy.html

@@ -25,9 +25,10 @@ <h2 class="preferred-set">Go!</h2>
 			<details id="set-preferred" open>
 				<summary>Select your Preferred Galaxy Server</summary>
 				<p class="card-text">
-					<a class="clickthrough btn btn-primary" href="https://usegalaxy.eu">UseGalaxy.eu 🌍🇪🇺</a>
-					<a class="clickthrough btn btn-primary" href="https://usegalaxy.org">UseGalaxy.org 🌎🇺🇸</a>
-					<a class="clickthrough btn btn-primary" href="https://usegalaxy.org.au">UseGalaxy.org.au 🌏</a>
+					{% assign servers = list_usegalaxy_servers_shuffle %}
+					{% for server in servers %}
+					<a class="clickthrough btn btn-primary" href="{{ server.url }}">{{ server.human }} ({{ server.id | upcase }})</a>
+					{% endfor %}
 					<button id="set-other" type="button" class="btn btn-secondary" data-toggle="modal" data-target="#exampleModal">Other</button>
 				</p>
 			</details>

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

@@ -28,8 +28,6 @@ contributors:
 
 In this section we will look at practical aspects of manipulation of next-generation sequencing data. We will start with the FASTQ format produced by most sequencing machines and will finish with the SAM/BAM format representing mapped reads. The cover image above shows a screen dump of a SAM dataset.
 
-# Introduction to sequencing data
-
 ## FASTQ manipulation and quality control
 
 [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) is not a very well defined format. In the beginning various manufacturers of sequencing instruments were free to interpret FASTQ as they saw fit, resulting in a multitude of FASTQ flavors. This variation stemmed primarily from different ways of encoding quality values as described [on the Wikipedia article for FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) (below you will find an explanation of quality scores and their meaning). Today, the [FASTQ Sanger](https://www.ncbi.nlm.nih.gov/pubmed/20015970) version of the format is considered to be the standard form of FASTQ. Galaxy is using FASTQ Sanger as the only legitimate input for downstream processing tools and provides [a number of utilities for converting FASTQ files](https://www.ncbi.nlm.nih.gov/pubmed/20562416) into this form (see **FASTQ Quality Control** section of Galaxy tools).
@@ -73,7 +71,7 @@ It is common to prepare pair-end and mate-pair sequencing libraries. This is hig
 
 Thus in both cases (paired-end and mate-pair) a single physical piece of DNA (or RNA in the case of RNA-seq) is sequenced from two ends and so generates two reads. These can be represented as separate files (two FASTQ files with first and second reads) or a single file were reads for each end are interleaved. Here are examples:
 
-#### Two single files
+### Two single files
 
 File 1
 
@@ -105,7 +103,7 @@ CACTACCGGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGTCCATC
 > Note that read IDs are **identical** in two files and they are listed in **the same** order. In some cases read IDs in the first and second file may be appended with `/1` and `/2` tags, respectively.
 {: .comment}
 
-#### Interleaved file
+### Interleaved file
 
 ```
 @1/1
@@ -448,7 +446,7 @@ 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