Merge pull request #4720 from galaxyproject/han-turtle

fix instance listing

_layouts/workflow-list.html

@@ -48,7 +48,7 @@ <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>
-			{% assign servers = list_usegalaxy_servers_shuffle %}
+			{% assign servers = nil | 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 %}

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 {% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}
+   - For example {% assign servers = nil | 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 ({% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %})
+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 = nil | 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

@@ -5,7 +5,7 @@
 ---
 
 <div class="row justify-content-md-center">
-	<div class="card col-md-6">
+	<div class="card col-md-6" style="padding: 0">
 		<div class="card-body">
 			<h1 class="h5 card-title" style="margin-top: 0">My Galaxy Training</h1>
 
@@ -25,7 +25,7 @@ <h2 class="preferred-set">Go!</h2>
 			<details id="set-preferred" open>
 				<summary>Select your Preferred Galaxy Server</summary>
 				<p class="card-text">
-					{% assign servers = list_usegalaxy_servers_shuffle %}
+					{% assign servers = nil | list_usegalaxy_servers_shuffle %}
 					{% for server in servers %}
 					<a class="clickthrough btn btn-primary" href="{{ server.url }}">{{ server.human }} ({{ server.id | upcase }})</a>
 					{% endfor %}

topics/admin/tutorials/introduction/slides.html

@@ -33,7 +33,7 @@
 
 # Where can Galaxy run?
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | list_usegalaxy_servers_shuffle %}
 
 * Cloud (SaaS)
   - A usegalaxy.* site: {% for server in servers %}[{{ server.human }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}

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

@@ -104,7 +104,7 @@ We will import the JSON files into Galaxy to query them directory, however the f
 >
 {: .comment}
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | list_usegalaxy_servers_shuffle %}
 
 > <hands-on-title>Loading SRA Aligned Read Format (SARF) Object Metadata URLs into Galaxy</hands-on-title>
 >

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

@@ -101,7 +101,7 @@
 
 # Find a Galaxy server
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | 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 +108,7 @@
 
 # Encuentra un servidor Galaxy
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | 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-reproduce/tutorial.md

@@ -40,7 +40,7 @@ For more background information about Galaxy, have a look into the Galaxy public
 
 # What does Galaxy look like?
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | 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.
 
 

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

@@ -245,7 +245,7 @@
 
 - Training materials: https://training.galaxyproject.org
 - Galaxy (an instructor will tell you which Galaxy to use)
-  {% assign servers = list_usegalaxy_servers_shuffle %}
+  {% assign servers = nil | list_usegalaxy_servers_shuffle %}
   {% for server in servers %}
   - {{ server.name }} {{ server.url }}
   {% endfor %}

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

@@ -82,7 +82,7 @@ This is a Galaxy tutorial based on material from the [COMBINE R RNAseq workshop]
 
 ## Import data from URLs
 
-{% assign servers = list_usegalaxy_servers_shuffle %}
+{% assign servers = nil | 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 %}.