Add Genome lab

subdomains/genome/CONTRIBUTORS

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+# If GitHub username, name and avatar will be fetched and displayed
+AnnaSyme
+neoformit

subdomains/genome/base.yml

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+# Test this locally with:
+# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/genome/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/genome/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
+lab_name: Genome Lab
+nationality: Australian
+galaxy_base_url: https://genome.usegalaxy.org.au  # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: genome
+root_domain: usegalaxy.org.au
+feedback_email: help@genome.edu.au
+
+# Custom content relative to this file URL
+header_logo: static/logo.png
+custom_css: static/custom.css
+intro_md: templates/intro.html
+conclusion_md: templates/conclusion.html
+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
+sections:
+  - data.yml
+  - assembly.yml
+  - annotation.yml

subdomains/genome/data.yml

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+id: data
+title: Data import and preparation
+tabs:
+  - id: tools
+    title: Tools
+    heading_md: >
+      Common tools are listed here, or search for more in the full tool panel to the left.
+    content:
+      - title_md: Import data to Galaxy
+        description_md: >
+          Standard upload of data to Galaxy, from your computer or from the web.
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+      - title_md: <code>FastQC</code> - sequence quality reports
+        description_md: >
+          <p>
+            Before using your sequencing data, it's important to ensure that
+            the data quality is sufficient for your analysis.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - bam
+              - sam
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc"
+      - title_md: <code>FastP</code> - sequence quality reports, trimming & filtering
+        description_md: >
+          <p>
+            Faster run than FastQC, this tool can also trim reads and filter by quality.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp"
+      - title_md: <code>NanoPlot</code> - visualize Oxford Nanopore data
+        description_md: >
+          <p>
+            A plotting suite for Oxford Nanopore sequencing data and alignments.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - fasta
+              - vcf_bgzip
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot"
+      - title_md: <code>GenomeScope</code> - estimate genome size
+        description_md: >
+          <p>
+            A set of metrics and graphs to visualize genome size and complexity prior to assembly.
+          </p>
+        inputs:
+          - datatypes:
+              - tabular
+            label: Output from <code>Meryl</code> or <code>Jellyfish histo</code>
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope"
+      - title_md: <code>Meryl</code> - count kmers
+        description_md: >
+          <p>
+            Prepare kmer count histogram for input to GenomeScope.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - fasta
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmeryl%2Fmeryl"
+  - id: workflows
+    title: Workflows
+    heading_md: >
+      A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
+      <a href="https://galaxyproject.org/learn/advanced-workflow/" target="_blank">Learn more.</a>
+    content:
+      - title_md: Data QC
+        description_md: >
+          <p>
+            Report statistics from sequencing reads. <br> <br> Tools: <code>nanoplot</code> <code>fastqc</code> <code>multiqc</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
+        view_link: https://workflowhub.eu/workflows/222
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+      - title_md: Kmer counting to estimate genome size
+        description_md: >
+          <p>
+            Estimates genome size and heterozygosity based on counts of kmers. <br> <br> Tools: <code>meryl</code> <code>genomescope</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=223"
+        view_link: https://workflowhub.eu/workflows/223
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+      - title_md: Trim and filter reads
+        description_md: >
+          <p>
+            Trims and filters raw sequence reads according to specified settings. <br> <br> Tools: <code>fastp</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=224"
+        view_link: https://workflowhub.eu/workflows/224
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+  - id: help
+    title: Help
+    content:
+      - title_md: How can I import my genomics data?
+        description_md: >
+          <p>
+            You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy. Just look for the "Upload data" button at the top of the tool panel.
+          </p>
+        button_md: More info
+        button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/
+      - title_md: How can I subsample my data?
+        description_md: >
+          <p>
+            We recommend subsampling large data sets to test tools and workflows. A useful tool is <code>seqtk_seq</code>, setting the parameter at "Sample fraction of sequences".
+          </p>
+      - title_md: How can I import data from the BPA portal?
+        description_md: >
+          <p>
+            BioPlatforms Australia allows data downloads via URL. Once you have generated one of these URLs in the BPA portal, you can import it into Galaxy using the "Fetch data" feature of the Upload tool.
+          </p>
+        button_md: More info
+        button_link: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly#in-depth-workflow-guide
+      - title_md: Can I upload sensitive data?
+        description_md: >
+          <p>
+            No, do not upload personal or sensitive, such as human health or clinical data. Please see our <a href="/about#data-privacy">Data Privacy</a> page for definitions of sensitive and health-related information.
+          </p>
+          <p>
+            Please also make sure you have read our <a href="/about#terms-of-service">Terms of Service</a>, which covers hosting and analysis of research data.
+          </p>
+      - title_md: Is my data private?
+        description_md: >
+          <p>
+            Please read our <a href="/about#data-privacy">Privacy Policy</a> for information on your personal data and any data that you upload.
+          </p>
+      - title_md: How can I increase my storage quota?
+        description_md: >
+          <p>
+            Please submit a quota request if your Galaxy Australia account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
+          </p>
+        button_md: Request
+        button_link: /request/quota
+      - title_md: "Tutorial: Quality Control"
+        description_md: >
+          <p>
+            Quality control and data cleaning is an essential first step in any NGS analysis. This tutorial will show you how to use and interpret results from <code>FastQC</code>, <code>NanoPlot</code> and <code>PycoQC</code>.
+          </p>
+        button_md: Tutorial
+        button_link: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html
+      - title_md: "Tutorial: introduction to Genomics and Galaxy"
+        description_md: >
+          <p>
+            This practical aims to familiarize you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.
+          </p>
+        button_md: Tutorial
+        button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html
+      - title_md: Galaxy Australia support
+        description_md: >
+          <p>
+            Any user of Galaxy Australia can request support through an online form.
+          </p>
+        button_md: Request support
+        button_link: /request/support

subdomains/genome/templates/conclusion.html

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+<section class="my-5">
+  <h4 class="mb-3">What's happening in {{ nationality }} genomics research?</h4>
+  <button
+    class="ga-btn"
+    data-bs-toggle="modal"
+    data-bs-target="#communityConnectModal"
+  >
+    Explore
+  </button>
+  <br>
+  <br>
+  <h4 class="mb-3">What do you think of the {{ lab_name }}?</h4>
+  <button
+    class="ga-btn"
+    data-bs-toggle="modal"
+    data-bs-target="#feedbackModal"
+  >
+    Give feedback
+  </button>
+</section>
+
+
+<div class="modal fade" id="feedbackModal" tabindex="-1">
+  <div class="modal-dialog modal-lg">
+    <div class="modal-content">
+      <form id="feedbackForm">
+
+        {% csrf_token %}
+
+        <div class="modal-header">
+          <h5 class="modal-title">Feedback</h5>
+          <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"
+            onclick="clearForm()"></button>
+        </div>
+        <div class="modal-body">
+          <div class="default-content">
+            <p>
+              We'd love to hear your feedback on the Galaxy Australia {{ site_name }}. Please let us know what
+              you think!
+            </p>
+            <div class="mb-3">
+              <label for="nameInput" class="form-label">Name</label>
+
+              <input type="text" class="form-control" id="nameInput" required>
+            </div>
+            <div class="mb-3">
+              <label for="emailInput" class="form-label">Email address</label>
+              <input type="email" class="form-control" id="emailInput" aria-describedby="emailHelp" required>
+              <div id="emailHelp" class="form-text">In case we'd like to contact you for more information.</div>
+            </div>
+            <div class="mb-3">
+              <label for="messageInput" class="form-label">Your feedback</label>
+              <textarea class="form-control" id="messageInput" rows="8" required></textarea>
+            </div>
+          </div>
+
+          <div class="success-content" style="display: none;">
+            <p class="alert alert-success">Thanks for your feedback!</p>
+          </div>
+
+          <div class="loading m-5 text-center" style="display: none;">
+            <img src="https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/static/home/img/spinner.svg" alt="Loading animation" width="150px">
+          </div>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" data-bs-dismiss="modal" onclick="clearForm();">Close</button>
+          <button type="submit" class="btn btn-primary">Submit</button>
+        </div>
+      </form>
+    </div>
+  </div>
+</div>
+
+<div class="modal fade" id="communityConnectModal" tabindex="-1">
+  <div class="modal-dialog modal-lg">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Australian genomics research</h5>
+        <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+      </div>
+      <div class="modal-body">
+        <p>
+          <p><a href="https://www.biocommons.org.au/genomics-domain" target="_blank">Discover more genomics activities and services supported by Australian BioCommons, and join in the community Genomics meetings</a></p>
+        </p>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+      </div>
+    </div>
+  </div>
+</div>
+
+
+<script>
+  function clearForm() {
+    setTimeout(() => {
+      document.getElementById('feedbackForm').reset();
+      $('#feedbackForm .default-content').show();
+      $('#feedbackForm .success-content').hide();
+      $('#feedbackForm .loading').hide();
+      $('button[type="submit"]').show();
+    }, 500);
+  }
+
+  function submitForm(event) {
+    event.preventDefault();
+    $('#feedbackForm .loading').show();
+    $('#feedbackForm .default-content').hide();
+    $('button[type="submit"]').hide();
+
+    // Clear any previous errors
+    $('#feedbackForm .error-message').remove();
+    $('#feedbackForm .invalid').removeClass('invalid');
+
+    let formData = new FormData();
+    formData.append('name', $('#nameInput').val());
+    formData.append('email', $('#emailInput').val());
+    formData.append('message', $('#messageInput').val());
+
+    fetch('/feedback/{{ subdomain }}', {
+      method: 'POST',
+      headers: {
+        'X-CSRFToken': getCsrfToken(),
+      },
+      body: formData,
+    }).then(r => r.json())
+      .then(data => {
+        if (data.success) {
+          showSuccess();
+        } else {
+          showErrors(JSON.parse(data.errors_json));
+        }
+      });
+  }
+
+  function getCsrfToken() {
+    return document.querySelector('[name=csrfmiddlewaretoken]').value;
+  }
+
+  function showSuccess() {
+    console.log("Form success");
+    $('#feedbackForm .loading').hide();
+    $('#feedbackForm .default-content').hide();
+    $('#feedbackForm .success-content').show();
+  }
+
+  function showErrors(errors) {
+    Object.keys(errors).forEach( (field) => {
+      errors[field].forEach( err => {
+        const msg = err.message;
+        $(`#${field}Input`)
+          .addClass('invalid')
+          .parent().append(`<small class="text-danger error-message">${msg}</small>`);
+      })
+    });
+    $('#feedbackForm .loading').hide();
+    $('#feedbackForm .default-content').show();
+    $('button[type="submit"]').show();
+  }
+
+  $('#feedbackForm').submit(submitForm);
+
+</script>

subdomains/genome/templates/footer.html

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+<iframe id="footerIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
+<script>
+  // Dynamically resize the iframe based on the content height
+  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>