Fix up proteomics lab

subdomains/proteomics/base.yml

@@ -1,22 +1,19 @@
-# Test this locally with:
-# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/proteomics/base.yml
-
 # Request this on site.usegalaxy.org.au with:
-# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/proteomics/base.yml
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/proteomics/base.yml
 
 # Check out the documentation for building exported labs:
 # https://site.usegalaxy.org.au/lab/export
 
 # Use these variables in HTML templates like:
 # "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
-# To make the content more generic and reusable across sites
-site_name: Australia
+# To make the content more generic and reusable across sites.
+site_name: ""
 lab_name: Proteomics Lab
-nationality: Australian
-galaxy_base_url: https://proteomics.usegalaxy.org.au  # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+nationality: ""
+galaxy_base_url: https://usegalaxy.org  # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
 subdomain: proteomics
-root_domain: usegalaxy.org.au
-feedback_email: help@genome.edu.au
+root_domain: usegalaxy.org
+# feedback_email: help@mygalaxy.org  # Set to enable feedback form
 
 # Custom content relative to this file URL
 header_logo: static/logo.png
@@ -28,11 +25,23 @@ footer_md: templates/footer.html
 # Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
 # Either:
 #   1. Relative to this file URL
-#   2. Full URL to fetch globally centralized content
+#   2. Full URL to fetch content from a different remote location
 sections:
   - sections/data.yml
   - sections/conversion_modification.yml
   - sections/database_searching.yml
   - sections/dda_standardised_tools.yml
   - sections/dia_standardised_tools.yml
   - sections/dda_tmt.yml
+
+# Histories listed here will be shown in a table
+# An empty list will remove this feature from the page
+shared_histories:
+  - url: https://usegalaxy.org.au/u/mike/h/lfq-and-tmt
+    label_html: >
+      Demo data for LFQanalyst and TMTanalyst.
+  - url: https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1
+    label_html: >
+      Example data provided for the "MaxQuant and MSstats for the analysis of
+      label-free data" Galaxy Training Network (GTN) tutorial, which is available
+      <a href="https://gxy.io/GTN:T00219">here</a>.

subdomains/proteomics/templates/conclusion.html

@@ -1 +0,0 @@
-{% include 'home/snippets/header-cards.html' %}

subdomains/proteomics/templates/footer.html

@@ -1,9 +0,0 @@
-<iframe id="footerIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
-<script>
-  window.addEventListener("message", function(event) {
-    const iframe = document.getElementById('footerIframe');
-    const height = event.data.height + 'px';
-    console.log('Set footer height:', height);
-    iframe.style.height = height;
-  }, false);
-</script>

subdomains/proteomics/templates/intro.html

@@ -8,7 +8,7 @@
     What is this page?
   </a>
   <p>
-    Welcome to the Galaxy Australia Proteomics Lab. Get quick access to the
+    Welcome to the {{ site_name }} {{ lab_name }}. Get quick access to the
     tools, workflows and tutorials you need to get started with proteomics on
     Galaxy.
   </p>
@@ -39,6 +39,7 @@
       </a>
     </div>
 
+    {% if shared_histories %}
     <div class="col">
       <a
         href="#"
@@ -57,6 +58,7 @@
         </table>
       </a>
     </div>
+    {% endif %}
   </div>
 </section>
 
@@ -91,12 +93,14 @@ <h5 class="modal-title">Galaxy {{ site_name }} {{ lab_name }}</h5>
           and {{ lab_name }}
           (<a href="galaxy_base_url">{{ subdomain }}.{{ root_domain }}</a>)
           is easy - look for the icon in the top navigation bar to switch between sites:
-          <img class="w-100 my-3 mx-auto" src="https://github.com/usegalaxy-au/galaxy-media-site/blob/dev/webapp/home/static/home/img/subdomains/site-switcher.png?raw=true" alt="Switch site button">
+          <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/subdomains/assets/site-switcher.png?raw=true" alt="Switch site button">
         </p>
 
+        {% if site_name == 'Australia' %}
         <p>
           <b>Please note:</b> unfortunately, AAF login is not configured for Galaxy Labs, but we are working on fixing this.
         </p>
+        {% endif %}
 
         <p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to the Base site</a></p>
       </div>
@@ -117,34 +121,22 @@ <h5 class="modal-title">Galaxy {{ site_name }} Shared Histories</h5>
       </div>
       <div class="modal-body">
         <p>
-          This set of proteomics-specific shared histories contain test or demo data for software available on Proteomics Lab. You can copy these histories directly to your account on Galaxy, making it faster to get started!
+          This set of proteomics-specific shared histories contain test or demo data for software available on {{ lab_name }}. You can copy these histories directly to your account on Galaxy, making it faster to get started!
         </p>
 
         <table class="table table-striped">
+          {% for history in shared_histories %}
           <tr>
             <td>
-              Demo data for LFQanalyst and TMTanalyst.
+              {{ history.label_html|safe }}
             </td>
             <td>
-              <a class="btn btn-primary text-nowrap" href="https://usegalaxy.org.au/u/mike/h/lfq-and-tmt">
-                View history
-              </a>
-            </td>
-          </tr>
-          <tr>
-            <td>
-              Example data provided for the "MaxQuant and MSstats for the analysis of label-free data" Galaxy Training Network (GTN) tutorial, which is available
-              <a href="https://gxy.io/GTN:T00219">here</a>.
-            </td>
-            <td>
-              <a
-                class="btn btn-primary text-nowrap"
-                href="https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1"
-              >
+              <a class="btn btn-primary text-nowrap" href="{{ history.url }}">
                 View history
               </a>
             </td>
           </tr>
+          {% endif %}
         </table>
       </div>
       <div class="modal-footer">

subdomains/proteomics/usegalaxy.org.au.yml

@@ -0,0 +1,32 @@
+# This content extends base.yml
+
+# Request this on site.usegalaxy.org.au with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/proteomics/usegalaxy.org.au.yml
+
+# Check out the documentation for building exported labs:
+# https://site.usegalaxy.org.au/lab/export
+
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites
+site_name: Australia
+lab_name: Proteomics Lab
+nationality: Australian
+galaxy_base_url: https://proteomics.usegalaxy.org.au  # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: proteomics
+root_domain: usegalaxy.org.au
+feedback_email: [email protected]
+
+# Custom content relative to this file URL
+conclusion_md: usegalaxy.org.au/templates/conclusion.html
+footer_md: usegalaxy.org.au/templates/footer.html
+
+shared_histories:
+  - url: https://usegalaxy.org.au/u/mike/h/lfq-and-tmt
+    label_html: >
+      Demo data for LFQanalyst and TMTanalyst.
+  - url: https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1
+    label_html: >
+      Example data provided for the "MaxQuant and MSstats for the analysis of
+      label-free data" Galaxy Training Network (GTN) tutorial, which is available
+      <a href="https://gxy.io/GTN:T00219">here</a>.

subdomains/proteomics/usegalaxy.org.au/templates/conclusion.html

@@ -0,0 +1 @@
+{% include 'home/snippets/header-cards.html' %}

subdomains/proteomics/usegalaxy.org.au/templates/footer.html

@@ -0,0 +1,9 @@
+<iframe id="footerIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
+<script>
+  window.addEventListener("message", function(event) {
+    const iframe = document.getElementById('footerIframe');
+    const height = event.data.height + 'px';
+    console.log('Set footer height:', height);
+    iframe.style.height = height;
+  }, false);
+</script>