Merge branch 'galaxyproject:main' into neoantigen

galaxyproject · Dec 13, 2024 · c4f4b54 · c4f4b54
2 parents 0e0948f + e229155
commit c4f4b54
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -70,6 +70,7 @@ jobs:
           make annotate ACTIVATE_ENV=pwd
           curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb
           curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
+          curl -L https://edamontology.org/EDAM.csv > metadata/EDAM.csv
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
           rdoc bin _plugins/ --output gtn_rdoc

diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -51,6 +51,7 @@ awspolly:
 
 # our real contributors <3 (please add yourself in alphabetical order)
 
+
 a-asai:
     name: Atsushi Asai
     email: [email protected]
@@ -86,6 +87,14 @@ abueg:
     orcid: 0000-0002-6879-3954
     joined: 2022-01
 
+adya29:
+    name: Adya Shreya
+    email: [email protected]
+    joined: 2024-12
+    linkedin: adya-shreya
+    location:
+      country: SG
+
 adairama:
     name: Adaikalavan Ramasamy
     email: [email protected]
@@ -95,6 +104,7 @@ adairama:
     location:
       country: SG
 
+
 ahmedhamidawan:
     name: Ahmed Hamid Awan
     email: [email protected]

diff --git a/GRANTS.yaml b/GRANTS.yaml
@@ -204,6 +204,27 @@ h2020-defend:
       This work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 773701.
     url: https://www.defend2020.eu
 
+nfdi4bioimage:
+    name:  NFDI4Bioimage
+    short_name: "NFDI4Bioimage"
+    github: false
+    joined: 2024-12
+    funding_id: "501864659"
+    funding_database: dfg
+    funder_name: DFG
+    url: https://nfdi4bioimage.de
+    avatar: "/training-material/shared/images/nfdi4bioimage.jpeg"
+
+nfdi4plants:
+    short_name: DataPLANT
+    name: DataPLANT (NFDI4Plants)
+    joined: 2024-07
+    funding_id: "442077441"
+    funding_database: dfg
+    funder_name: DFG
+    url:  https://nfdi4plants.org
+    avatar: "/training-material/shared/images/logo-dataplant.svg"
+
 nhgri-anvil:
     name: National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space
     short_name: "NHGRI ANVIL"
@@ -235,3 +256,6 @@ skills4eosc:
 
 
 
+
+
+
diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml
@@ -39,6 +39,14 @@ deNBI:
     name: de.NBI
     url: https://www.denbi.de/
 
+dfg:
+    name:  Deutsche Forschungsgemeinschaft
+    short_name: "DFG"
+    github: false
+    joined: 2024-12
+    url: https://www.dfg.de/de
+    avatar: "/training-material/shared/images/DFG_grant.png"
+
 earlham:
     name: Earlham Institute
     joined: 2017-09
@@ -208,13 +216,6 @@ ncbi:
     avatar: "/training-material/shared/images/ncbi.png"
     ror: "02meqm098"
 
-nfdi4plants:
-    short_name: DataPLANT
-    name: DataPLANT (NFDI4Plants)
-    joined: 2024-07
-    url:  https://nfdi4plants.org
-    avatar: "/training-material/shared/images/logo-dataplant.svg"
-
 NIH:
     name: National Institutes of Health
     short_name: "NIH"
@@ -363,9 +364,3 @@ vib:
     github: false
     ror: "03xrhmk39"
 
-nfdi4bioimage:
-    short_name: NFDI4BIOIMAGE
-    name: NFDI4BIOIMAGE
-    joined: 2024-11
-    url:  https://nfdi4bioimage.de
-    avatar: "/training-material/shared/images/nfdi4bioimage.jpeg"
diff --git a/_includes/cyoa-choices.html b/_includes/cyoa-choices.html
@@ -1,6 +1,8 @@
 <blockquote class="notranslate hands_on gtn-cyoa" id="gtn-cyoa{{ include.disambiguation }}">
-	<div class="box-title" aria-label="hands-on box: choose your own tutorial"><i class="fas fa-pencil-alt" aria-hidden="true"></i><span class="visually-hidden"></span> Hands-on: Choose Your Own Tutorial</div>
+	<div class="box-title" aria-label="hands-on box: choose your own tutorial"><i class="fas fa-pencil-alt" aria-hidden="true"></i><span class="visually-hidden"></span> {{ include.title | default: "Hands-on: Choose Your Own Tutorial" }}</div>
+	{% unless include.brief %}
 	<p>This is a "Choose Your Own Tutorial" section, where you can select between multiple paths. Click one of the buttons below to select how you want to follow the tutorial</p>
+	{% endunless %}
 	{% if include.text %}
 	<p>
 		{{ include.text }}

diff --git a/_layouts/by_tool.html b/_layouts/by_tool.html
@@ -2,60 +2,103 @@
 layout: base
 ---
 
-{% assign tool_id_path = page.observed_tool_ids[0][0] %}
+{% assign tool_id_path = page.latest_tool_id %}
 
 <hgroup>
 	<h1>
 		{{ site.data['tool-meta'][tool_id_path].name }}:
 		{{ site.data['tool-meta'][tool_id_path].desc }}
 	</h1>
-	<pre>{{ page.observed_tool_ids[0] }}</pre>
+	<pre>{{ tool_id_path }}</pre>
 </hgroup>
 
 <section>
 	<div class="stats">
 		<div class="row">
 			<div class="col-md-3">
 				<h2>Metadata</h2>
-				<h3>Servers Offering this Tool</h3>
-				<a href="https://usegalaxy.eu/?tool_id={{ page.observed_tool_ids[0][0] }}">UseGalaxy.eu ({{ page.observed_tool_ids[0][1] }})</a>
-				<p class="text-muted">This is a guess, we are not currently checking if that is actually present.</p>
 
-				<hgroup>
-					<h3>Observed Tool Versions</h3>
-					<p>Within GTN tutorials</p>
-				</hgroup>
+				<h3>Links</h3>
 				<ul>
-					{% for tool in page.observed_tool_ids %}
-					<li>{{ tool[1] }}</li>
-					{% endfor %}
+					{% if site.data['tool-meta'][tool_id_path]['bio.tools'] %}
+					<li>
+						<a href="https://bio.tools/{{ site.data['tool-meta'][tool_id_path]['bio.tools'] }}">
+						bio.tools: {{ site.data['tool-meta'][tool_id_path]['bio.tools_name'] }}
+						</a>
+					</li>
+					{% endif %}
+					{% if site.data['toolshed-revisions'][tool_id] %}
+					<li>
+						{% assign repo_info = site.data['toolshed-revisions'][tool_id] %}
+						<a href="https://toolshed.g2.bx.psu.edu/view/{{ repo_info[0] }}/{{ repo_info[1] }}/{{ repo_info[2] }}">
+						Galaxy ToolShed Repository
+						</a>
+					</li>
+					{% endif %}
 				</ul>
 
-				{% if site.data['tool-meta'][tool_id_path].edam_operations %}
+				{% assign edam_op_count = site.data['tool-meta'][tool_id_path].edam_operations | size %}
+				{% if edam_op_count > 0 %}
 				<h3>EDAM Operations</h3>
 				<ul>
 				{% for topic in site.data['tool-meta'][tool_id_path].edam_operations %}
 					<li>
+						{% assign edam_info = topic | edamify: site %}
 						<a href="https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252F{{ topic }}">
-						{{ topic }}
+							{{ edam_info['Preferred Label'] | default: topic }}
 						</a>
 					</li>
 				{% endfor %}
 				</ul>
 				{% endif %}
 
-				{% if site.data['tool-meta'][tool_id_path].edam_topics%}
+				{% assign edam_topic_count = site.data['tool-meta'][tool_id_path].edam_topics | size %}
+				{% if edam_topic_count > 0 %}
 				<h3>EDAM Topics</h3>
 				<ul>
 				{% for topic in site.data['tool-meta'][tool_id_path].edam_topics %}
 					<li>
+						{% assign edam_info = topic | edamify: site %}
 						<a href="https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252F{{ topic }}">
-						{{ topic }}
+							{{ edam_info['Preferred Label'] | default: topic }}
 						</a>
 					</li>
 				{% endfor %}
 				</ul>
 				{% endif %}
+
+				<hgroup>
+					<h3>Observed Tool Versions</h3>
+					<p>Within GTN tutorials</p>
+				</hgroup>
+
+				{% for tool in page.observed_tool_ids %}
+				<details>
+					<summary>{{ tool[1] }}</summary>
+					{% assign v_id = tool[0] %}
+					{% assign supported = site | tool_version_support: v_id %}
+					{% assign usegalaxy_exact = supported.exact | where: "usegalaxy", "true"   %}
+					{% assign other_exact = supported.exact | where: "usegalaxy", "false"   %}
+
+					<ul>
+						{% for inst in usegalaxy_exact %}
+						<li>
+							<a href="{{ inst.url }}?tool_id={{ tool[0] }}&version={{ tool[1] }}">
+								{{ inst.name }} <abbr title="This is a UseGalaxy.* server which meets minimum requirements for a public Galaxy">⭐️</abbr>
+							</a>
+						</li>
+						{% endfor %}
+						{% for inst in other_exact %}
+						<li>
+								<a href="{{ inst.url }}?tool_id={{ tool[0] }}&version={{ tool[1] }}">
+								{{ inst.name }}
+							</a>
+						</li>
+						{% endfor %}
+					</ul>
+				</details>
+				{% endfor %}
+
 			</div>
 
 			<div class="col-md-9">
@@ -74,3 +117,21 @@ <h2>Relevant Tutorials</h2>
 		</div>
 	</div>
 </section>
+
+<style>
+details {
+	border: 1px solid black;
+	margin-bottom: 0.2rem;
+	cursor: pointer;
+
+	summary {
+		padding: 0.5rem
+	}
+}
+details:hover {
+	box-shadow: 5px 5px var(--brand-color)
+}
+details:active {
+	box-shadow: 3px 3px var(--brand-color)
+}
+</style>
diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html
@@ -249,8 +249,8 @@ <h3> GitHub Activity</h4>
 		{% if page.gh_prs_count > 0 %}
 		<h4>{{ page.gh_prs_count }} Merged Pull Requests</h4>
 		<p>
-		See all of the 
-                <a href="https://github.com/galaxyproject/training-material/pulls?q=is%3Apr+author%3A{{page.contributor}}">{% icon github %} Pull Requests</a> and 
+		See all of the
+                <a href="https://github.com/galaxyproject/training-material/pulls?q=is%3Apr+author%3A{{page.contributor}}">{% icon github %} Pull Requests</a> and
 		<a href="https://github.com/galaxyproject/training-material/commits?author={{page.contributor}}">{% icon github %} Commits</a> by {{ entity.name | default: page.contributor }}.
 		</p>
 		<ul>
@@ -350,15 +350,23 @@ <h2>External Links</h2>
 				{% endif %}
 
 				{% if entity.funding_id %}
-					Grant ID:
+                <div class="contact-items">
+                    <p><b>Funding information</b>
+                    {% if entity.funder_name %}
+                    <br>Funding body: {{entity.funder_name}}
+                    {% endif %}
+					<br>Grant ID:
 					{% if entity.funding_database %}
 						{% assign url = entity | fetch_funding_url %}
 						<a href="{{ url }}">
 							{{ entity.funding_id }}
 						</a>
 					{% else %}
-						{{ entity.funding_id }}
+						<br>{{ entity.funding_id }}
 					{% endif %}
+
+                    </p>
+                </div>
 				{% endif %}
 
 				{% if entity.email %}
@@ -424,9 +432,9 @@ <h2>External Links</h2>
 				</div>
 				{% endif %}
 
-				<p>Favourite Topics</p>
+				<p><b>Favourite Topics</b></p>
 				<canvas id="myChart" height="300px"></canvas>
-				<p>Favourite Formats</p>
+				<p><b>Favourite Formats</b></p>
 				<canvas id="slidesVsTutorials" height="300px"></canvas>
 
 			</div>

diff --git a/_layouts/home.html b/_layouts/home.html
@@ -209,12 +209,11 @@ <h2>Contributor Hall of Fame</h2>
         <div class="col-lg-5 col-md-5 col-sm-12">
 
 		<h2>Quickstart</h2>
-
 		<div class="button-group">
-<a href="{% link learning-pathways/index.md %}" class="btn home-cta-button"><div>Learning Pathways</div><img alt="A scientist with a hair bun passes accepts a flask from a small grey creature" src="{% link assets/images/galaxy-for-scientists.svg %}" style="height: 5rem"></a>
-<a href="{% link topics/admin/index.md %}" class="btn home-cta-button"><div>Galaxy for SysAdmins</div><img alt="a person sits at a computer with baudot code in the backgorund" src="{% link assets/images/galaxy-for-admins.svg %}" style="height: 5rem"></a>
-<a href="{% link topics/dev/index.md %}" class="btn home-cta-button"><div>Galaxy for Developers</div><img alt="a small person leans against a large laptop" src="{% link assets/images/galaxy-for-developers.svg %}" style="height: 5rem"></a>
-<a href="{% link topics/teaching/index.md %}" class="btn home-cta-button"><div>Galaxy for Teachers</div><img alt="a person stands in front of a blackboard" src="{% link assets/images/galaxy-for-trainers.svg %}" style="height: 5rem"></a>
+<a href="{% link learning-pathways/index.md %}?utm_source=gtn&utm_medium=home&utm_campaign=home-quickstart" class="btn home-cta-button"><div>Learning Pathways</div><img alt="A scientist with a hair bun passes accepts a flask from a small grey creature" src="{% link assets/images/galaxy-for-scientists.svg %}" style="height: 5rem"></a>
+<a href="{% link topics/admin/index.md %}?utm_source=gtn&utm_medium=home&utm_campaign=home-quickstart" class="btn home-cta-button"><div>Galaxy for SysAdmins</div><img alt="a person sits at a computer with baudot code in the backgorund" src="{% link assets/images/galaxy-for-admins.svg %}" style="height: 5rem"></a>
+<a href="{% link topics/dev/index.md %}?utm_source=gtn&utm_medium=home&utm_campaign=home-quickstart" class="btn home-cta-button"><div>Galaxy for Developers</div><img alt="a small person leans against a large laptop" src="{% link assets/images/galaxy-for-developers.svg %}" style="height: 5rem"></a>
+<a href="{% link topics/teaching/index.md %}?utm_source=gtn&utm_medium=home&utm_campaign=home-quickstart" class="btn home-cta-button"><div>Galaxy for Teachers</div><img alt="a person stands in front of a blackboard" src="{% link assets/images/galaxy-for-trainers.svg %}" style="height: 5rem"></a>
 </div>
 
 

diff --git a/_layouts/learning-pathway.html b/_layouts/learning-pathway.html
@@ -44,6 +44,23 @@ <h3 id="st-{{ section.section | slugify }}">{{ section.section }}</h3>
 
 	{% if section.tutorials %}
         {% assign material_list = site | convert_to_material_list: section.tutorials %}
+	<p><strong>{% icon time aria=false %} {{ locale['time-estimation'] | default: "Time estimation"}}:</strong> {{ material_list | sum_duration }}</p>
+	<details>
+		<summary>Learning Objectives</summary>
+		<ul>
+		{% if section.learning_objectives %}
+			{% for lo in section.learning_objectives %}
+			<li>{{ lo }}</li>
+			{% endfor %}
+		{% else %}
+		{% for material in material_list %}
+			{% for lo in material.objectives %}
+			<li>{{ lo }}</li>
+			{% endfor %}
+		{% endfor %}
+		{% endif %}
+		</ul>
+	</details>
 	{% include _includes/tutorial_list.html sub=material_list %}
 	{% endif %}
     {% endfor %}