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assembly community resources update
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‎communities/assembly/lab/CONTRIBUTORS‎

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# If GitHub username, name and avatar will be fetched and displayed
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#Include here the key contributors
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# alphabetical order
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#Include here other contributors

‎communities/assembly/lab/README.md‎

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# Community subdomain/Lab

‎communities/assembly/lab/base.yml‎

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# Request this as a webpage with:
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# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/galaxyproject/galaxy_codex/tree/main/communities/<community-name>/base.yml
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# -----------------------------------------------------------------------------
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# Use these variables in HTML templates like:
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# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
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# To make the content more generic and reusable across sites
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# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!"
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site_name: European
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lab_name: Community Lab
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analysis_name: community
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nationality: European
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# Used for rendering tool/workflow links. Trailing '/' will be removed.
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# TODO !! {{ lab_name }} below needs to be replaced manually
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galaxy_base_url: https://{{ lab_name }}.usegalaxy.eu
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subdomain: {{ lab_name }}
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root_domain: usegalaxy.eu
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support_url: https://help.galaxyproject.org/
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general_support: https://galaxyproject.org/support/
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#figure_microbiome_url: https://github.com/usegalaxy-eu/microgalaxy_paper_2025/blob/main/docs/figures/figure_1_B.png?raw=true
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# This will enable a feedback form on the webpage:
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# feedback_email: help@mygalaxy.org
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quota_request_url: https://help.galaxyproject.org
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data_policy_url: https://usegalaxy.org/static/terms.html
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terms_url: https://usegalaxy.org/static/terms.html
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galaxy_help_url: https://help.galaxyproject.org
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gtn_slack_url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg
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#gtn_matrix_channel: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im
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galaxy_matrix_channel: https://matrix.to/#/#galaxyproject_Lobby:gitter.im
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european_server_matrix_channel: https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im
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#figure_isolates_url: https://github.com/usegalaxy-eu/microgalaxy_paper_2025/blob/main/docs/figures/figure_1_A.png?raw=true
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#microgalaxy_matrix: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im
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help_links:
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- title: General Galaxy support
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url: https://galaxyproject.org/support/
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- title: General Galaxy help forum
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url: https://help.galaxyproject.org
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- title: Galaxy Training Network Slack workspace
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url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg
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- title: Galaxy Training Community chat
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url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im
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- title: Usegalaxy.org chat
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url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im
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# - title: microGalaxy user community chat room (Same channel but using Matrix/Element)
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# url: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im
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intro_extra_md: ""
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conclusion_extra_md: ""
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# -----------------------------------------------------------------------------
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# Custom content relative to this file URL
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#header_logo: microgalaxy-logo.png
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intro_md: intro.html
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conclusion_md: conclusion.html
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#Currently empty:
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#footer_md: footer.html
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#custom_css: custom.css
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# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
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# Either:
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# 1. Relative to this file URL
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# 2. Full URL to fetch globally centralized content
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sections:
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#Sections created (and updated) automatically
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- sections/1_data_import_and_preparation.yml
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- sections/2_tools.yml
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- sections/3_workflows.yml
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- sections/4_tutorials.yml
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- sections/5_support_and_help.yml
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- sections/6_community.yml
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#Sections that are community specific (created manually)
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# - sections/2_microbial_isolates.yml
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# - sections/3_microbiome.yml
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# -----------------------------------------------------------------------------

‎communities/assembly/lab/conclusion.html‎

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{% load markdown %}
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<!-- <section class="my-5">
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{% if help_links %}
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<h4 class="mb-3">{{ lab_name }} community support</h4>
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<ul>
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{% for link in help_links %}
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<li>
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<a href="{{ link.url }}" target="_blank">{{ link.title }}</a>
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</li>
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{% endfor %}
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</ul>
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{% endif %}
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</section>
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<section>
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<h4 class="mb-3">News and Events</h4>
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<div class="row justify-content-center">
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe>
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</div>
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe>
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</div>
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</div>
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</section> -->
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{% if feedback_email %}
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<section class="my-5">
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<h4 class="my-3">What do you think of the {{ lab_name }}?</h4>
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<button
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class="ga-btn"
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data-bs-toggle="modal"
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data-bs-target="#feedbackModal"
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>
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Give feedback
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</button>
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</section>
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{% endif %}
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<section class="my-5">
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<h4 class="mb-3">Cite Us</h4>
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</section>
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<section class="my-5">
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If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage.
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<!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>-->
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</section>
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<section id="conclusionExtra">
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{{ conclusion_extra_md|safe }}
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</section>

‎communities/assembly/lab/intro.html‎

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<section class="my-5" id="tagline">
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<p>
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Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
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</p>
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<p>
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#Here include an intro to your page, see the ex mple below from the microgalaxy community
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# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p>
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<p>
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<a
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href="#"
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data-bs-toggle="modal"
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data-bs-target="#infoModal">
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How does this page relate to Galaxy {{ site_name }}?
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</a>
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</p>
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{{ intro_extra_md }}
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<div class="modal fade" id="infoModal" tabindex="-1">
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<div class="modal-dialog modal-lg">
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<div class="modal-content">
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<div class="modal-header">
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<h5 class="modal-title">Galaxy {{ site_name }}</h5>
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<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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</div>
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<div class="modal-body">
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<p>
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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 {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
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</p>
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<p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
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<p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
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<p><a class="ga-btn" href="{{support}}">Galaxy {{ site_name }} support</a></p>
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</div>
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<div class="modal-footer">
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<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
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</div>
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</div>
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</div>
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</div>
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</section>

‎communities/assembly/lab/sections/1_data_import_and_preparation.yml‎

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id: data
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title: Getting started
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tabs:
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- id: data-import
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title: Data import
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heading_md: >
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Common tools that allow for data import.
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content:
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- title_md: Import data to Galaxy
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description_md: >
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Standard upload of data to Galaxy, from your computer or from the web.
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
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button_tip: Upload Data
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- title_md: Download data from NCBI GenBank/RefSeq
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description_md: >
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Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download"
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button_tip: Download Data from NCBI
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- title_md: Download raw reads from NCBI SRA
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description_md: >
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Faster Download and Extract Reads in FASTQ format from NCBI SRA
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump"
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button_tip: Download raw reads from NCBI SRA
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- title_md: Download run data from EBI SRA
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description_md: >
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ENA data can be searched and retrieved interactively and programmatically and visualized using this ENA Browser tool
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button_link: "https://www.ebi.ac.uk/ena/browser/search"
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button_tip: Download run data from EBI SRA
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- title_md: Download run data from UCSC
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description_md: >
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Use this tool to retrieve and export data from the Genome Browser annotation track database
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button_link: "https://genome.ucsc.edu/cgi-bin/hgTables"
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button_tip: Download run data from UCSC
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# - id: highlight-tools
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# title: Highlight tools
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# heading_md: >
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# Flagship tools for <your-community>
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# content:
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# - title_md: <code>Bakta</code> - Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
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# description_md: >
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# A tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and Metagenomic Assembled Genomes (MAGs).
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# inputs:
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# - datatypes:
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# - fasta
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# button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta"
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# - id: interactive-tools
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# title: Interactive tools
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# heading_md: >
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# Interactive tools for <your-community>
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# content:
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# - title_md: <code>Pavian</code> - Interactive analysis of metagenomics data
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# description_md: >
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# An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
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# inputs:
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# - datatypes:
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# - Kraken report
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# - MetaPhlAn report
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# button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian"
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# - id: learning-pathways
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# title: Learning pathways
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.
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# content:
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# - title_md: Introduction to Galaxy and Sequence analysis
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# description_md: >
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# New to Galaxy and/or the field of genomics? In this learning pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.
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# button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html
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# button_icon: tutorial
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# button_tip: Open Learning Pathway
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.

‎communities/assembly/lab/sections/2_tools.yml‎

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id: tools
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title: Community curated tools
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tabs: []

‎communities/assembly/lab/sections/3_workflows.yml‎

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id: workflows
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title: Community curated workflows
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tabs:
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- id: iwc
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content: []
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- id: other_workflowhub
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content: []
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- id: gtn
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content: []
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- id: public
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content: []

‎communities/assembly/lab/sections/4_tutorials.yml‎

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id: tutorials
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title: Community curated tutorials
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tabs: []

‎communities/assembly/lab/sections/5_support_and_help.yml‎

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id: support
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title: Support & Help
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tabs:
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- id: help
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title: Help
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heading_md: >
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You can request help through different channels. If you think your problem might help other users as well,
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please post it in the Galaxy Help Forum. Please report tool bugs through our
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[support channel]({{ support_url }})
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and for specific questions feel free to reach out via the matrix chat.
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content:
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- title_md: Troubleshooting
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description_md: >
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Find specific advice for
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{gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)
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on the GTN.
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- title_md: Galaxy Support
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description_md: >
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Any user of Galaxy {{ site_name }} can request support online!
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button_md: Request support
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button_link: "{{ support_url }}"
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button_icon: help
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button_tip: Request support
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# - title_md: microGalaxy chat room
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# description_md: >
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# Chat with members of the microGalaxy community on Matrix
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# button_link: "{{ microgalaxy_matrix }}"
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# button_md: Matrix channel
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# button_icon: social
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# button_tip: Join the chat
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- id: faq
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title: FAQ
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content:
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- title_md: How can I increase my storage quota?
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description_md: >
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Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
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button_md: Request
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button_link: "{{ quota_request_url }}"
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button_tip: Request quota
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button_icon: help
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- title_md: Can I upload sensitive data?
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description_md: >
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No, please do not upload personal or sensitive, such as human health or clinical data. Please see our
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[Privacy Policy]({{ data_policy_url }})
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page for definitions of sensitive and health-related information.
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Please also make sure you have read our
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[Terms of Service]({{ terms_url }}),
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which covers hosting and analysis of research data.
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- title_md: Is my data private?
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description_md: >
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Please read our
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[Privacy Policy]({{ data_policy_url }})
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for information on your personal data and any data that you upload.

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