Add microGalaxy lab

communities/all/labs/microgalaxy

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+../../microgalaxy/lab

communities/microgalaxy/lab/CONTRIBUTORS

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+# If GitHub username, name and avatar will be fetched and displayed
+bebatut
+zierep
+EngyNasr

communities/microgalaxy/lab/README.md

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+# microGalaxy subdomain/Lab
+

communities/microgalaxy/lab/base.yml

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+# Request this as a webpage with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/base.yml
+
+# -----------------------------------------------------------------------------
+# 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
+
+# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!"
+site_name: European
+lab_name: microGalaxy Lab
+analysis_name: microGalaxy
+nationality: European
+
+# Used for rendering tool/workflow links. Trailing '/' will be removed.
+galaxy_base_url: https://microgalaxy.usegalaxy.eu
+subdomain: microGalaxy
+root_domain: usegalaxy.eu
+
+# This will enable a feedback form on the webpage:
+# feedback_email: [email protected]
+
+support_url: https://help.galaxyproject.org
+quota_request_url: https://help.galaxyproject.org
+data_policy_url: https://usegalaxy.org/static/terms.html
+terms_url: https://usegalaxy.org/static/terms.html
+
+help_links:
+  - title: General Galaxy support
+    url: https://galaxyproject.org/support/
+  - title: General Galaxy help forum
+    url: https://help.galaxyproject.org
+  - title: Galaxy Training Network Slack workspace
+    url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg
+  - title: microGalaxy user community chat room (Same channel but using Matrix/Element)
+    url: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im
+  - title: Galaxy Training Community chat
+    url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im
+  - title: Usegalaxy.org chat
+    url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im
+
+intro_extra_md: ""
+conclusion_extra_md: ""
+
+# -----------------------------------------------------------------------------
+# Custom content relative to this file URL
+
+header_logo: static/microgalaxy-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:
+  - sections/1_data_import_and_preparation.yml
+  - sections/2_microbial_isolates.yml
+  - sections/3_microbiome.yml
+  - sections/4_tools.yml
+  - sections/5_workflows.yml
+  - sections/6_support_and_help.yml
+  - sections/7_community.yml
+
+# -----------------------------------------------------------------------------

communities/microgalaxy/lab/sections/1_data_import_and_preparation.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: tutorials
+    title: Tutorials
+    heading_md: >
+
+    content: []
+
+  - id: faq
+    title: FAQ
+    heading_md: >
+
+    content: []

communities/microgalaxy/lab/sections/2_microbial_isolates.yml

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+id: isolates
+title: Microbial isolates
+tabs:
+  - id: workflows
+    title: Workflows
+    heading_md: >
+
+    content: []
+
+  - id: tutorials
+    title: Tutorials
+    heading_md: >
+
+    content: []
+
+  - id: pathways
+    title: Learning pathways
+    heading_md: >
+       Connected tutorials to train you to perform microbial data analysis fast!.
+    content:
+      - title_md: Introduction to Galaxy and Sequence analysis
+        description_md: >
+          New to Galaxy and/or the field of genomics? In this learing 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.
+        button_link: 
+      - title_md: Genome annotation for prokaryotes
+        description_md: >
+
+        button_link: 
+      - title_md: Detection of AMR genes in bacterial genomes
+        description_md: >
+
+        button_link: 
+
+  - id: faq
+    title: FAQ
+    heading_md: >
+
+    content: []

communities/microgalaxy/lab/sections/3_microbiome.yml

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+id: microbiome
+title: Microbiome
+tabs:
+  - id: workflows
+    title: Workflows
+    heading_md: >
+
+    content: []
+
+  - id: tutorials
+    title: Tutorials
+    heading_md: >
+
+    content: []
+
+  - id: pathways
+    title: Learning pathways
+    heading_md: >
+       Connected tutorials to train you to perform microbial data analysis fast!.
+    content:
+      - title_md: Introduction to Galaxy and Sequence analysis
+        description_md: >
+          New to Galaxy and/or the field of genomics? In this learing 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.
+        button_link: 
+      - title_md: Metagenomics data processing and analysis for microbiome
+        description_md: >
+
+        button_link: 
+      - title_md: Clinical metaproteomics workflows within Galaxy
+        description_md: >
+
+        button_link: 
+
+  - id: faq
+    title: FAQ
+    heading_md: >
+
+    content: []