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Add microGalaxy lab (#263)
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* Add 1st draft for the microgalaxy lab

* tool list

* tool list

* add link

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* multiple tools

* remote tools

* test

* test

* test

* bla

* bla

* All tools

* changing to the new structure of excalidraw, content still need to be filled

* changing base and usegalaxy servers yml files

* correcting file name

* solving linting errors

* changing 2 links to microGalaxy

* updating with microGalaxy logo

* changing news and events source link

* correcting links

* removing github microGalaxy link

* Apply suggestions from code review

applying comments

Co-authored-by: Bérénice Batut <berenice.batut@gmail.com>

* updating links

* adding help links to the lab in the community section as a third tab

* changing from links to buttons

* commenting the news and events section for now and commenting the bottom helping links since we have them aready in the community section

* correcting the bottons shaps

* updating bottons shapes

* Delete communities/microgalaxy/resources/.~lock.curated_tools.tsv#

* Update communities/microgalaxy/lab/base.yml

Co-authored-by: Bérénice Batut <bebatut@gmail.com>

---------

Co-authored-by: paulzierep <paul.zierep@googlemail.com>
Co-authored-by: EngyNasr <engynasr94@gmail.com>
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3 people authored Dec 18, 2024
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1 change: 1 addition & 0 deletions communities/all/labs/microgalaxy
4 changes: 4 additions & 0 deletions communities/microgalaxy/lab/CONTRIBUTORS
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# If GitHub username, name and avatar will be fetched and displayed
bebatut
zierep
EngyNasr
2 changes: 2 additions & 0 deletions communities/microgalaxy/lab/README.md
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# microGalaxy subdomain/Lab

68 changes: 68 additions & 0 deletions 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/galaxyproject/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: help@mygalaxy.org

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

# -----------------------------------------------------------------------------
110 changes: 110 additions & 0 deletions 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: []
38 changes: 38 additions & 0 deletions 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: []
38 changes: 38 additions & 0 deletions 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: []
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