Merge pull request #167 from neoformit/add-labs

Add Genome and Proteomics labs

communities/all/labs/genome

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+../../genome/lab/

communities/all/labs/proteomics

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+../../proteomics/lab/

communities/all/labs/single-cell

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+../../spoc/lab/

communities/all/labs/spoc

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+../../spoc/lab/

communities/genome/lab/CONTRIBUTORS

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

communities/genome/lab/base.yml

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+# 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/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: ""
+lab_name: Genome Lab
+nationality: ""
+galaxy_base_url: https://genome.usegalaxy.org  # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: genome
+root_domain: usegalaxy.org
+# feedback_email: [email protected]  # set to enable feedback form
+
+# 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 content from a different remote location
+sections:
+  - data.yml
+  - assembly.yml
+  - annotation.yml

communities/genome/lab/data.yml

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+id: data
+title: Data import and preparation
+tabs:
+  - id: help
+    title: Overview
+    heading_md: >
+      If you are new to galaxy, uploading your data is a good place to start!
+      <br>
+      Check out the Tools and Workflows tabs for different approaches to uploading data.
+    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
+  - 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

communities/genome/lab/templates/intro.html

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+<section class="my-5" id="tagline">
+  <p>
+    Welcome to the Galaxy {{ site_name }} {{ lab_name }}. Get quick access to tools, workflows and tutorials for genome assembly and annotation.
+    <br>
+    <a
+      href="#"
+      data-bs-toggle="modal"
+      data-bs-target="#infoModal">
+      What is this page?
+    </a>
+  </p>
+
+  <div class="modal fade" id="infoModal" tabindex="-1">
+    <div class="modal-dialog modal-lg">
+      <div class="modal-content">
+        <div class="modal-header">
+          <h5 class="modal-title">Galaxy {{ site_name }}</h5>
+          <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+        </div>
+        <div class="modal-body">
+          <p>
+            This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ nationality }} researchers. Your history, jobs and data quota are shared with the "Base" website.
+          </p>
+
+          <div class="my-3">
+            Switch between sites quickly using the dropdown in Galaxy {{ site_name }}'s main navigation bar (note, if your Galaxy server does not have this, please request that they install the "Site Switcher" plugin from Galaxy Australia):
+            <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/labs/assets/site-switcher.png?raw=true" alt="Switch site button">
+          </div>
+
+          <p><a class="ga-btn" href="{{ galaxy_base_url }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
+          <p><a class="ga-btn" href="/about">What is Galaxy {{ site_name }}?</a></p>
+          <p><a class="ga-btn" href="/request/support">Galaxy {{ site_name }} support</a></p>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+        </div>
+      </div>
+    </div>
+  </div>
+</section>

communities/genome/lab/usegalaxy.org.au.yml

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+# 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/genome/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: 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: [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