Merge branch 'galaxyproject:main' into patch-5

CONTRIBUTORS.yaml

@@ -1253,6 +1253,13 @@ npalopoli:
     name: Nicolas Palopoli
     joined: 2021-09
 
+npechl:
+    name: Nikolaos Pechlivanis
+    email: [email protected]
+    twitter: npechl
+    joined: 2023-05
+    orcid: 0000-0003-2502-612X
+
 nsoranzo:
     name: Nicola Soranzo
     matrix: 'nsoranzo:matrix.org'

_config.yml

@@ -145,7 +145,7 @@ icon-tag:
   hands_on: fas fa-pencil-alt
   help: far fa-question-circle
   history-annotate: fas fa-comment
-  history-share: fas fa-toggle-on
+  history-share: fas fa-share-alt
   instances: fas fa-globe
   interactive_tour: fas fa-magic
   keypoints: fas fa-key

_includes/default-header.html

@@ -22,9 +22,11 @@
                             {% icon topic aria=false %} {{ topic.title }}
                         </a>
                         {% else %}
+			{% if page.path == 'index.md' %}
                         <a class="nav-link" href="{{ site.baseurl }}/hall-of-fame" title="Hall of Fame">
                            {% icon hall-of-fame %} Contributors
                         </a>
+			{% endif %}
 
                         {% endif %}
                     </li>

_includes/extras.html

@@ -1,54 +1,66 @@
 <li class="nav-item dropdown">
-    <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" aria-expanded="false" title="Extras">
-        {% icon galaxy-star %} Extras
+    <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" aria-expanded="false" title="Settings">
+	{% icon galaxy-gear %} Settings
     </a>
     <div class="dropdown-menu dropdown-menu-right">
 
-        <a class="dropdown-item" href="{{ site.github_repository }}/edit/{{ site.github_repository_branch }}/{{ page.path }}" title="Edit on GitHub">
-          {% icon github %} Edit on GitHub
+	<h6 class="dropdown-header">Preferences</h6>
+
+	<a href="{% link user/theme.md %}" class="dropdown-item">
+		{% icon gtn-theme %} Theme
+	</a>
+
+	<a href="{% link user/privacy.md %}" class="dropdown-item">
+		{% icon pref-dataprivate %} Data Privacy
+	</a>
+
+	<div class="dropdown-divider"></div>
+
+	<h6 class="dropdown-header">For Everyone</h6>
+
+        <a class="dropdown-item" href="{{ site.github_repository }}/edit/{{ site.github_repository_branch }}/{{ page.path }}">
+          {% icon github %} Propose a change or correction
         </a>
 
-        <a class="dropdown-item" href="{% link stats.md %}" title="Show view statistics about this repository">
+	<h6 class="dropdown-header">Instructor Utilities</h6>
+
+        <a class="dropdown-item" href="{% link stats.md %}">
             {% icon galaxy-barchart %} GTN statistics
         </a>
 
-        <a class="dropdown-item" href="https://plausible.galaxyproject.eu/training.galaxyproject.org?period=12mo&page={{site.baseurl}}{{ page.url }}" title="Show view statistics of this page">
-            {% icon galaxy-barchart %} Page Metrics
+        <a class="dropdown-item" href="https://plausible.galaxyproject.eu/training.galaxyproject.org?period=12mo&page={{site.baseurl}}{{ page.url }}">
+            {% icon galaxy-barchart %} Page View Metrics
         </a>
 
         <!-- link to feedback -->
         {% if page.layout == 'topic' %}
             {% assign fdbk_by_topic = site.data['feedback'] | how_many_topic_feedbacks:site.data[page.topic_name].title %}
             {% if fdbk_by_topic > 0 %}
-                <a class="dropdown-item" href="{{ site.baseurl }}/feedback.html#topic-{{ page.topic_name }}" title="Show feedback statistics about this topic">
+                <a class="dropdown-item" href="{{ site.baseurl }}/feedback.html#topic-{{ page.topic_name }}">
                     {% icon galaxy-barchart %} Topic feedback
                 </a>
             {% else %}
-                <a class="dropdown-item" href="{% link feedback.md %}" title="Show feedback statistics about this repository">
+                <a class="dropdown-item" href="{% link feedback.md %}">
                     {% icon galaxy-barchart %} GTN feedback
                 </a>
             {% endif %}
         {% elsif page.layout == 'tutorial_hands_on' %}
             {% assign fdbk_by_tutorial = site.data['feedback'] | how_many_tutorial_feedbacks:page.title %}
             {% if fdbk_by_tutorial > 0}
-                <a class="dropdown-item" href="{{ site.baseurl }}/feedback.html#tutorial-{{ page.tutorial_name }}" title="Show feedback statistics about this tutorial">
+                <a class="dropdown-item" href="{{ site.baseurl }}/feedback.html#tutorial-{{ page.tutorial_name }}">
                     {% icon galaxy-barchart %} Tutorial feedback
                 </a>
             {% else %}
-                <a class="dropdown-item" href="{% link feedback.md %}" title="Show feedback statistics about this repository">
+                <a class="dropdown-item" href="{% link feedback.md %}">
                     {% icon galaxy-barchart %} GTN feedback
                 </a>
             {% endif %}
         {% else %}
-            <a class="dropdown-item" href="{% link feedback.md %}" title="Show feedback statistics about this repository">
+            <a class="dropdown-item" href="{% link feedback.md %}">
                 {% icon galaxy-barchart %} GTN feedback
             </a>
         {% endif %}
 
-		<a href="{% link preferences.md %}" class="dropdown-item">
-			{% icon gtn-theme %} User Preferences <span class="badge badge-secondary">New</span>
-		</a>
-
         <div class="dropdown-item">
             <div>
                 {% icon galaxy-rulebuilder-history %} Previous Versions

_layouts/workflow-list.html

@@ -25,7 +25,10 @@ <h6 class="card-subtitle mb-2 text-muted">
 				<small class="text-muted">Last updated {{ workflow.path | gtn_mod_date | date: "%b %-d, %Y" }}</small>
 			</p>
 			<p class="card-text">
-			<span tabindex="0" role="button" class="workflow show-when-galaxy-proxy-active" data-workflow="{{ workflow.trs_endpoint }}">Launch in Tutorial Mode</span><br/>
+			<span tabindex="0" role="button" class="workflow show-when-galaxy-proxy-active" data-workflow="{{ workflow.trs_endpoint }}">Launch in Tutorial Mode</span>
+			<a href="{% link faqs/galaxy/tutorial_mode.md %}" class="hide-when-galaxy-proxy-active">{% icon question %}</a>
+			<br/>
+
 
 			License: 
 				{% if workflow.license %}
@@ -38,13 +41,19 @@ <h6 class="card-subtitle mb-2 text-muted">
 			Tests: {% if workflow.tests %}✅{% else %}❌{% endif %}
 			Results: {% if workflow.test_results == nil %}Not yet automated{% endif %}
 			</p>
-
-			<a href="{{ site.url }}{{ site.baseurl }}/{{ workflow.path }}" class="btn btn-primary">Download Galaxy Workflow.ga</a>
-			<a href="https://usegalaxy.eu/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-secondary hide-when-galaxy-proxy-active">EU</a>
-			<a href="https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-secondary hide-when-galaxy-proxy-active">US</a>
-			<a href="https://usegalaxy.org.au/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="btn btn-secondary hide-when-galaxy-proxy-active">AU</a>
+<div class="dropdown">
+  <button class="btn btn-primary dropdown-toggle" type="button" data-toggle="dropdown" aria-expanded="false">
+    Import or Download
+  </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>
 			<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>
+			   class="dropdown-item hide-when-galaxy-proxy-active">Import to another server (≥23.0+ only!)</a>
+  </div>
+</div>
 
 	</div>
 	<pre class="mermaid">{{ workflow.mermaid }}

assets/css/main.scss

@@ -915,24 +915,30 @@ blockquote {
 
 // This applies a "dark" style to the dropdown menus on small devices since
 // Bootstrap v4 does not do that by default.
+
+.dropdown-menu {
+	background-color: var(--color-background);
+	border-color: var(--border);
+}
+.dropdown-item {
+	color: var(--text-color);
+
+	&:hover, &:focus, &:active {
+		background-color: var(--brand-color);
+		color:  var(--text-color);
+	}
+}
+
+.dropdown-divider {
+	border-top-color: var(--border);
+}
+
 @media (max-width: 768px) {
     .navbar {
         .dropdown-menu {
-		background-color: var(--color-background);
             border-color: transparent;
         }
 
-        .dropdown-item {
-		color: var(--text-color);
-
-            &:hover,
-            &:focus,
-            &:active {
-                background-color: var(--brand-color);
-                color:  var(--text-color);
-            }
-        }
-
         .nav-item,
         .dropdown-item {
             overflow: hidden;
@@ -1593,6 +1599,10 @@ ul.text-list, ol.text-list {
 .dropdown-item:focus-visible {
 }
 
+.dropdown-header {
+	color: var(--text-color-muted);
+}
+
 ol.breadcrumb {
 	background: var(--secondary-color);
 
@@ -1682,6 +1692,7 @@ figure > a[target="_blank"]::after {
 	figure {
 		max-width: 20em;
 		margin: 0rem 0.5rem;
+		border: 0px transparent;
 
 		img {
 			max-height: 5em;

bin/schema-tutorial.yaml

@@ -187,6 +187,12 @@ mapping:
             link on Zenodo to the input data for the tutorial
         examples:
             - "https://zenodo.org/record/3706539"
+    extra:
+        type: map
+        description: |
+            Any additional variables you want to set on the page
+        mapping:
+          '=': {}
     tags:
         type: seq
         sequence:

faqs/galaxy/histories_sharing.md

@@ -9,6 +9,7 @@ contributors: [shiltemann]
 
 Sharing your history allows others to import and access the datasets, parameters, and steps of your history.
 
+Access the history sharing menu via the History Options dropdown ({% icon galaxy-history-options %}), and clicking "{% icon history-share %} Share or Publish"
 
 1. **Share via link**
    - Open the **History Options** {% icon galaxy-gear %} menu (gear icon) at the top of your history panel and select **Share or Publish**

metadata/shortlinks.yaml

@@ -488,6 +488,8 @@ name:
   visualisation/circos-microbial: "/topics/visualisation/tutorials/circos-microbial/tutorial.html"
   single-cell/EBI-retrieval: "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html"
   visualisation/bad-graphs/slides: "/topics/visualisation/tutorials/bad-graphs/slides.html"
+  climate/ocean-data-view: "/topics/climate/tutorials/ocean-data-view/tutorial.html"
+  climate/ocean-variables: "/topics/climate/tutorials/ocean-variables/tutorial.html"
 id:
   T00000: "/topics/admin/tutorials/ansible/tutorial.html"
   T00001: "/topics/admin/tutorials/ansible-galaxy/tutorial.html"
@@ -1420,6 +1422,13 @@ id:
   N00061: "/news/2023/11/20/workflow-search.html"
   N00062: "/news/2023/11/21/mastodon.html"
   N00063: "/news/2023/11/21/video.html"
+  T00375: "/topics/climate/tutorials/ocean-data-view/tutorial.html"
+  T00376: "/topics/climate/tutorials/ocean-variables/tutorial.html"
+  F00362: "/faqs/galaxy/analysis_getting_help.html"
+  F00363: "/faqs/galaxy/datasets_upload_from_genomeark.html"
+  F00364: "/faqs/galaxy/workflows_import_from_dockstore.html"
+  F00365: "/topics/assembly/tutorials/vgp_genome_assembly/faqs/dataset_upload_fasta_via_urls.html"
+  F00366: "/topics/assembly/tutorials/vgp_genome_assembly/faqs/dataset_upload_fastqsanger_via_urls.html"
 misc:
   ansible-galaxy: "/topics/admin/tutorials/ansible-galaxy/tutorial.html"
   stats: "/stats.html"

topics/climate/tutorials/fates-jupyterlab/tutorial.md

@@ -506,17 +506,7 @@ p.fig.savefig('CANOPY_HEIGHT_DIST.png')
 
 One of the most important features of Galaxy comes at the end of an analysis. When you have published striking findings, it is important that other researchers are able to reproduce your in-silico experiment. Galaxy enables users to easily share their workflows and histories with others.
 
-To share a history, click on the {% icon galaxy-gear %} icon in the history panel and select `Share or Publish`. On this page you can do 3 things:
-
-1. **Make History Accessible via Link**. This generates a link that you can give out to others. Anybody with this link will be able to view your history.
-2. **Make History Accessible and Publish**. This will not only create a link, but will also publish your history. This means your history will be listed under `Shared Data → Histories` in the top menu.
-3. **Share with a user**. This will share the history only with specific users on the Galaxy instance.
-
-> <comment-title>Permissions</comment-title>
-> Different servers have different default permission settings. Some servers create all of your datasets completely private to you, while others make them accessible if you know the secret ID.
->
-> Be sure to select **Also make all objects within the History accessible** whenever you make a history accessible via link, otherwise whomever you send your link to might not be able to see your history.
-{: .comment}
+{% snippet faqs/galaxy/histories_sharing.md %}
 
 > <hands-on-title>Share history</hands-on-title>
 >

topics/climate/tutorials/fates/tutorial.md

@@ -392,17 +392,7 @@ We would like to run a CLM-FATES case where the atmospheric Carbon Dioxyde Conce
 
 One of the most important features of Galaxy comes at the end of an analysis. When you have published striking findings, it is important that other researchers are able to reproduce your in-silico experiment. Galaxy enables users to easily share their workflows and histories with others.
 
-To share a history, click on the {% icon galaxy-gear %} icon in the history panel and select `Share or Publish`. On this page you can do 3 things:
-
-1. **Make History Accessible via Link**. This generates a link that you can give out to others. Anybody with this link will be able to view your history.
-2. **Make History Accessible and Publish**. This will not only create a link, but will also publish your history. This means your history will be listed under `Shared Data → Histories` in the top menu.
-3. **Share with a user**. This will share the history only with specific users on the Galaxy instance.
-
-> <comment-title>Permissions</comment-title>
-> Different servers have different default permission settings. Some servers create all of your datasets completely private to you, while others make them accessible if you know the secret ID.
->
-> Be sure to select **Also make all objects within the History accessible** whenever you make a history accessible via link, otherwise whomever you send your link to might not be able to see your history.
-{: .comment}
+{% snippet faqs/galaxy/histories_sharing.md %}
 
 > <hands-on-title>Share history</hands-on-title>
 >

topics/climate/tutorials/ocean-variables/tutorial.bib

@@ -0,0 +1,53 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}
+
+@misc{hcmrdata,
+  doi = {10.13120},
+  url = {https://doi.org/10.13120/a51003ee-d2ab-4b6c-a4ca-c95d1d872018},
+  author = {{Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC)}},
+  keywords = {oceans, environment, global ocean observing system,  ocean circulation,  in-situ,  ocean pressure,  sea water salinity,  sea water temperature,  multi-year,  weather climate and seasonal observation,  global-ocean},
+  title = {Mediterranean Sea - Eutrophication and Acidity aggregated datasets 1911/2022 v2022},
+  publisher = {EMODnet Chemistry},
+  year = {2022},
+  copyright = {Creative Commons Attribution 4.0 International}
+}