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Codex community layout #590

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6c31438
Create the needed files for communities tool
scorreard Feb 5, 2026
20256bb
Automatising tutorials pages (1/2)
scorreard Feb 5, 2026
6572bf0
New code and template to create the community pages for the codex
scorreard Feb 5, 2026
fd5e067
Change organizeImports setting to true
scorreard Feb 5, 2026
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2 changes: 1 addition & 1 deletion .vscode/settings.json
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Expand Up @@ -6,4 +6,4 @@
"source.organizeImports": true
}
},
}
}
20 changes: 19 additions & 1 deletion _data/topnav.yml
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Expand Up @@ -9,4 +9,22 @@ subitems:
url: /training
- title: About
url: /about

#Community specific links:
- title: Microbiome
subitems:
- title: Tools
url: /microgalaxy_tools
- title: Workflows
url: /microgalaxy_workflows
- title: Tutorials
url: /microgalaxy_tutorials
#Community specific links are added manually when a lab is created to ensure communities are ready to display them
#To add a community specific tab, copy/paste the template below and replace with you community name and generate a PR
#- title: <Community name>
# subitems:
# - title: Tools
# url: /<community-name>_tools
# - title: Workflows
# url: /<community-name>_workflows
# - title: Tutorials
# url: /<community-name>_tutorials
108 changes: 108 additions & 0 deletions _includes/communities/microgalaxy/tools.html
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{%- if include.tag %}
{%- assign tools = site.data.communities.microgalaxy.curated_tools | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %}
{%- else %}
{%- assign tools = site.data.communities.microgalaxy.curated_tools | add_related_pages | sort_natural: "name" %}
{%- endif %}
{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
{%- unless tools.size == 0 or tools == nil %}
<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
<div class="table-responsive mt-4 mb-5">
<table class="tooltable table display table-bordered table-striped w-100">
<thead>
<tr>
<th style="text-align: center">Suite ID</th>
<th style="text-align: center">Suite version</th>
<th style="text-align: center">Date of first commit of the suite</th>
<th style="text-align: center">Tool IDs</th>
<th style="text-align: center">Description</th>
<th style="text-align: center">EDAM topic(s)</th>
<th style="text-align: center">EDAM operation(s)</th>
<th style="text-align: center">Suite runs on main servers</th>
<th style="text-align: center">bio.tools (if available)</th>
<th style="text-align: center">Conda id</th>
<th style="text-align: center">biii</th>
<th style="text-align: center">Status</th>
<th style="text-align: center">Availability across Galaxies</th>
</tr>
</thead>
<tbody>
{%- for tool in tools %}
<tr>
<td>
<div>
{% if tool.["Suite ID"] != "" %}
<a href='{{ tool.["Suite source"] }}'>{{ tool.["Suite ID"] }}</a>
{% else %}
<a href="#">{{ tool.["Suite ID"] }}</a>
{% endif %}
</div>
</td>
<td style="text-align: center">{{tool.["Suite version"]}}</td>
<td style="text-align: center">{{tool.["Date of first commit of the suite"]}}</td>
<td style="text-align: center">
{% if tool.["Tool IDs"] %} {%- for id in tool.["Tool IDs"] %}
<span class="badge text-bg-light">
{{id}}
</span>
{%- endfor %} {%- endif %}
</td>
<td>{{tool.Description}}</td>
<td style="text-align: center">
{% if tool.["EDAM topics"] %} {%- for topic in tool.["EDAM topics"] %}
<span class="badge text-bg-light">
{{topic}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">
{% if tool.["EDAM operations"] %} {%- for operation in tool.["EDAM operations"] %}
<span class="badge text-bg-light">
{{operation}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">{{tool.["Suite runs on main servers"]}}</td>
<td style="text-align: center">
<div>
{% if tool.["bio.tool ID"] != "null" %}
<a href='https://bio.tools/{{ tool.["bio.tool ID"] }}'>{{ tool.["bio.tool ID"] }}</a>
{% else %}
<a href="#">""</a>
{% endif %}
</div>
</td>
<td style="text-align: center">
<div>
{% if tool.["Suite conda package"] != "null" %}
<span class="badge text-bg-light">
{{ tool.["Suite conda package"] }}
</span>
{% endif %}
</div>
</td>
<td style="text-align: center">
<div>
{% if tool.["biii ID"] != "null" %}
<span class="badge text-bg-light">
{{ tool.["biii ID"] }}
</span>
{% endif %}
</div>
</td>
<td>{{tool.["Suite version status"]}}</td>
<td>
<div>
{% if tool.availability %} {%- for instance in tool.availability %}
<span class="badge text-bg-light">
{{instance}}
</span>
{%- endfor %} {%- endif %}
</div>
</td>
</tr>
{%- endfor %}
</tbody>
</table>
</div>
{%- endunless %}
<div id="skip-tool-table"></div>
60 changes: 60 additions & 0 deletions _includes/communities/microgalaxy/tutorials.html
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{%- if include.tag %}
{%- assign tools = site.data.communities.microgalaxy.tutorials | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %}
{%- else %}
{%- assign tools = site.data.communities.microgalaxy.tutorials | add_related_pages | sort_natural: "name" %}
{%- endif %}
{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
{%- unless tools.size == 0 or tools == nil %}
<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
<div class="table-responsive mt-4 mb-5">
<table class="tooltable table display table-bordered table-striped w-100">
<thead>
<tr>
<th style="text-align: center">Title (+link)</th>
<th style="text-align: center">GTN topic name</th>
<th style="text-align: center">Last updated</th>
<th style="text-align: center">EDAM topic(s)</th>
<th style="text-align: center">EDAM operation(s)</th>
<th style="text-align: center">Resources available</th>
</tr>
</thead>
<tbody>
{%- for tool in tools %}
<tr>
<td>
<div>
{% if tool.title != "" %}
<a href='{{ tool.url }}'>{{ tool.title }}</a>
{% else %}
<a href="#">{{ tool.title }}</a>
{% endif %}
</div>
</td>
<td style="text-align: center">{{ tool.topic_name_human }}</td>
<td style="text-align: center">{{ tool.mod_date }}</td>
<td style="text-align: center">
{% if tool.edam_topic %} {%- for topic in tool.edam_topic %}
<span class="badge text-bg-light">
{{topic}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">
{% if tool.edam_operation %} {%- for operation in tool.edam_operation %}
<span class="badge text-bg-light">
{{operation}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">
{% if tool.slides %}<span class="badge text-bg-light">Slides</span>{%- endif %}
{% if tool.video %}<span class="badge text-bg-light">Video</span>{%- endif %}
{% if tool.hands_on %}<span class="badge text-bg-light">Hands-on</span>{%- endif %}
</td>
</tr>
{%- endfor %}
</tbody>
</table>
</div>
{%- endunless %}
<div id="skip-tool-table"></div>
76 changes: 76 additions & 0 deletions _includes/communities/microgalaxy/workflows.html
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{%- if include.tag %}
{%- assign tools = site.data.communities.microgalaxy.curated_workflows | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %}
{%- else %}
{%- assign tools = site.data.communities.microgalaxy.curated_workflows | add_related_pages | sort_natural: "name" %}
{%- endif %}
{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
{%- unless tools.size == 0 or tools == nil %}
<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
<div class="table-responsive mt-4 mb-5">
<table class="tooltable table display table-bordered table-striped w-100">
<thead>
<tr>
<th style="text-align: center">Workflow name (+link)</th>
<th style="text-align: center">Creation time</th>
<th style="text-align: center">Last updated</th>
<th style="text-align: center">License</th>
<th style="text-align: center">EDAM topic(s)</th>
<th style="text-align: center">EDAM operation(s)</th>
<th style="text-align: center">Tag(s)</th>
<th style="text-align: center">DOI</th>
<th style="text-align: center">Source</th>
</tr>
</thead>
<tbody>
{%- for tool in tools %}
<tr>
<td>
<div>
{% if tool.name != "" %}
<a href='{{ tool.link }}'>{{ tool.name }}</a>
{% else %}
<a href="#">{{ tool.name }}</a>
{% endif %}
</div>
</td>
<td style="text-align: center">{{ tool.create_time }}</td>
<td style="text-align: center">{{ tool.update_time }}</td>
<td style="text-align: center">{{ tool.license }}</td>
<td style="text-align: center">
{% if tool.edam_topic %} {%- for topic in tool.edam_topic %}
<span class="badge text-bg-light">
{{topic}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">
{% if tool.edam_operation %} {%- for operation in tool.edam_operation %}
<span class="badge text-bg-light">
{{operation}}
</span>
{%- endfor %} {%- endif %}
</td>
<td style="text-align: center">
{% if tool.tags %} {%- for tag in tool.tags %}
<span class="badge text-bg-light">
{{tag}}
</span>
{%- endfor %} {%- endif %}
</td>
<td>
<div>
{% if tool.doi != "null" %}
<a href='{{ tool.doi }}'>DOI</a>
{% else %}
""
{% endif %}
</div>
</td>
<td style="text-align: center">{{ tool.source }}</td>
</tr>
{%- endfor %}
</tbody>
</table>
</div>
{%- endunless %}
<div id="skip-tool-table"></div>
11 changes: 11 additions & 0 deletions pages/microgalaxy_tools.md
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---
title: Tools
description: An interactive list of Galaxy tools created by the Galaxy CoDex for a specific community.
datatable: true
sidebar: false
toc: false
---

<div markdown="0">
{% include communities/microgalaxy/tools.html %}
</div>
11 changes: 11 additions & 0 deletions pages/microgalaxy_tutorials.md
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---
title: Tutorials
description: An interactive list of Galaxy tutorials created by the Galaxy CoDex for a specific community.
datatable: true
sidebar: false
toc: false
---

<div markdown="0">
{% include communities/microgalaxy/tutorials.html %}
</div>
11 changes: 11 additions & 0 deletions pages/microgalaxy_workflows.md
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---
title: Workflows
description: An interactive list of Galaxy workflows created by the Galaxy CoDex for a specific community.
datatable: true
sidebar: false
toc: false
---

<div markdown="0">
{% include communities/microgalaxy/workflows.html %}
</div>
7 changes: 7 additions & 0 deletions sources/bin/get_community_tools.sh
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Expand Up @@ -35,6 +35,13 @@ for com_data_fp in communities/* ; do
if [[ -e "communities/$community/resources/curated_tools.yml" ]]; then
mkdir -p _data/communities/$community/
ln -sf ../../../communities/$community/resources/curated_tools.yml _data/communities/$community/curated_tools.yml
#For pages - Can't copy from template, need to copy from existing md file
cp pages/microgalaxy_tools.md pages/${community}_tools.md
sed -i -e "s/microgalaxy/${community}/g" pages/${community}_tools.md
#For _includes - To keep same process as above, copying from existing file
mkdir -p _includes/communities/$community/
cp _includes/communities/microgalaxy/tools.html _includes/communities/$community/tools.html
sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/tools.html
fi;

if [[ -e "communities/$community/resources/curated_tools.tsv" ]]; then
Expand Down
7 changes: 7 additions & 0 deletions sources/bin/get_community_tutorials.sh
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Expand Up @@ -21,6 +21,13 @@ for com_data_fp in communities/* ; do
if [[ -f "communities/$community/resources/tutorials.yml" ]]; then
mkdir -p _data/communities/$community/
ln -sf ../../../communities/$community/resources/tutorials.yml _data/communities/$community/tutorials.yml
#For pages - Can't copy from template, need to copy from existing md file
cp pages/microgalaxy_tutorials.md pages/${community}_tutorials.md
sed -i -e "s/microgalaxy/${community}/g" pages/${community}_tutorials.md
#For _includes - To keep same process as above, copying from existing file
mkdir -p _includes/communities/$community/
cp _includes/communities/microgalaxy/tutorials.html _includes/communities/$community/tutorials.html
sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/tutorials.html
fi;

if [[ -e "communities/$community/resources/tutorials.tsv" ]]; then
Expand Down
7 changes: 7 additions & 0 deletions sources/bin/get_community_workflows.sh
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Expand Up @@ -31,6 +31,13 @@ for com_data_fp in communities/* ; do
if [[ -f "communities/$community/metadata/curated_workflows.yml" ]]; then
mkdir -p _data/communities/$community/
ln -sf ../../../communities/$community/resources/curated_workflows.yml _data/communities/$community/curated_workflows.yml
#For pages - Can't copy from template, need to copy from existing md file
cp pages/microgalaxy_workflows.md pages/${community}_workflows.md
sed -i -e "s/microgalaxy/${community}/g" pages/${community}_workflows.md
#For _includes - To keep same process as above, copying from existing file
mkdir -p _includes/communities/$community/
cp _includes/communities/microgalaxy/workflows.html _includes/communities/$community/workflows.html
sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/workflows.html
fi;

if [[ -e "communities/$community/resources/curated_workflows.tsv" ]]; then
Expand Down