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spoc community automatic resources update #671

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53 changes: 53 additions & 0 deletions communities/spoc/lab/conclusion.html
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{% load markdown %}

<!-- <section class="my-5">
{% if help_links %}
<h4 class="mb-3">{{ lab_name }} community support</h4>
<ul>
{% for link in help_links %}
<li>
<a href="{{ link.url }}" target="_blank">{{ link.title }}</a>
</li>
{% endfor %}
</ul>
{% endif %}
</section>

<section>
<h4 class="mb-3">News and Events</h4>

<div class="row justify-content-center">
<div class="col">
<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe>
</div>
<div class="col">
<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe>
</div>
</div>
</section> -->

{% if feedback_email %}
<section class="my-5">
<h4 class="my-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>
{% endif %}

<section class="my-5">
<h4 class="mb-3">Cite Us</h4>
</section>

<section class="my-5">
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.
<!-- 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>-->
</section>

<section id="conclusionExtra">
{{ conclusion_extra_md|safe }}
</section>
41 changes: 41 additions & 0 deletions communities/spoc/lab/intro.html
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<section class="my-5" id="tagline">
<p>
Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
</p>

<p>
#Here include an intro to your page, see the ex mple below from the microgalaxy community
# 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>
<p>
<a
href="#"
data-bs-toggle="modal"
data-bs-target="#infoModal">
How does this page relate to Galaxy {{ site_name }}?
</a>
</p>

{{ intro_extra_md }}

<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 {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
</p>
<p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
<p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
<p><a class="ga-btn" href="{{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>
74 changes: 74 additions & 0 deletions communities/spoc/lab/sections/1_data_import_and_preparation.yml
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id: data
title: Getting started
tabs:
- id: data-import
title: Data import
heading_md: >
Common tools that allow for data import.
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"
button_tip: Upload Data
- title_md: Download data from NCBI GenBank/RefSeq
description_md: >
Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API
button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download"
button_tip: Download Data from NCBI
- title_md: Download raw reads from NCBI SRA
description_md: >
Faster Download and Extract Reads in FASTQ format from NCBI SRA
button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump"
button_tip: Download raw reads from NCBI SRA
- title_md: Download run data from EBI SRA
description_md: >
ENA data can be searched and retrieved interactively and programmatically and visualized using this ENA Browser tool
button_link: "https://www.ebi.ac.uk/ena/browser/search"
button_tip: Download run data from EBI SRA
- title_md: Download run data from UCSC
description_md: >
Use this tool to retrieve and export data from the Genome Browser annotation track database
button_link: "https://genome.ucsc.edu/cgi-bin/hgTables"
button_tip: Download run data from UCSC

# - id: highlight-tools
# title: Highlight tools
# heading_md: >
# Flagship tools for <your-community>
# content:
# - title_md: <code>Bakta</code> - Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
# description_md: >
# A tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and Metagenomic Assembled Genomes (MAGs).
# inputs:
# - datatypes:
# - fasta
# button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta"

# - id: interactive-tools
# title: Interactive tools
# heading_md: >
# Interactive tools for <your-community>
# content:
# - title_md: <code>Pavian</code> - Interactive analysis of metagenomics data
# description_md: >
# 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.
# inputs:
# - datatypes:
# - Kraken report
# - MetaPhlAn report
# button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian"

# - id: learning-pathways
# title: Learning pathways
# heading_md: >
# Connected tutorials to train you to perform microbial data analysis.
# content:
# - title_md: Introduction to Galaxy and Sequence analysis
# description_md: >
# 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.
# button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html
# button_icon: tutorial
# button_tip: Open Learning Pathway
# heading_md: >
# Connected tutorials to train you to perform microbial data analysis.
190 changes: 190 additions & 0 deletions communities/spoc/lab/sections/2_tools.yml
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id: tools
title: Community curated tools
tabs:
- id: clustering
title: Clustering
heading_md: 'Top 10 most used tools* for the EDAM operation: Clustering <br> *based
on usage statistics from Galaxy’s main servers over the last five years'
content:
- title_md: gsc_scran_normalize
description_md: |-
Normalize raw counts using scran
(Tool usage: 616)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=scran_normalize">scran_normalize</a></li>
</ul>
- title_md: infercnv
description_md: |-
Infer Copy Number Variation from Single-Cell RNA-Seq Data
(Tool usage: 31)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=infercnv">infercnv</a></li>
</ul>
- title_md: gsc_filter_cells
description_md: |-
Filter single cell RNAseq data on library depth and number of detected genes
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=filter_cells">filter_cells</a></li>
</ul>
- title_md: gsc_filter_genes
description_md: |-
Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=filter_genes">filter_genes</a></li>
</ul>
- title_md: gsc_gene_expression_correlations
description_md: |-
Compute single-cell paire-wise gene expressions correlations
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=single_cell_gene_expression_correlations">single_cell_gene_expression_correlations</a></li>
</ul>
- title_md: gsc_high_dimensions_visualisation
description_md: |-
Generates PCA, t-SNE and HCPC visualisation
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=high_dimensions_visualisation">high_dimensions_visualisation</a></li>
</ul>
- title_md: gsc_mannwhitney_de
description_md: |-
Perform a mann-whitney differential testing between two sets of gene expression data
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=mannwhitney_de">mannwhitney_de</a></li>
</ul>
- title_md: gsc_signature_score
description_md: |-
Compute signature scores from single cell RNAseq data
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=signature_score">signature_score</a></li>
</ul>
- id: no_associated_edam_operation
title: No associated EDAM operation
heading_md: 'Top 10 most used tools* for the EDAM operation: No associated EDAM
operation <br> *based on usage statistics from Galaxy’s main servers over the
last five years'
content:
- title_md: volcanoplot
description_md: |-
Tool to create a Volcano Plot
(Tool usage: 126750)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=volcanoplot">volcanoplot</a></li>
</ul>
- title_md: anndata
description_md: |-
Import, Export, Inspect and Manipulate Anndata and Loom objects
(Tool usage: 87208)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_export">anndata_export</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_import">anndata_import</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_inspect">anndata_inspect</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_manipulate">anndata_manipulate</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=modify_loom">modify_loom</a></li>
</ul>
- title_md: seurat
description_md: |-
Seurat - R toolkit for single cell genomics
(Tool usage: 10776)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_create">seurat_create</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_data">seurat_data</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_integrate">seurat_integrate</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_clustering">seurat_clustering</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_preprocessing">seurat_preprocessing</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_plot">seurat_plot</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_reduce_dimension">seurat_reduce_dimension</a></li>
</ul>
- title_md: sceasy
description_md: |-
Convert scRNA data object between popular formats
(Tool usage: 2488)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=sceasy_convert">sceasy_convert</a></li>
</ul>
- title_md: deseq2_normalization
description_md: |-
Normalizes gene hitlists
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=deseq2_normalization">deseq2_normalization</a></li>
</ul>
- id: rna-seq_analysis
title: RNA-Seq analysis
heading_md: 'Top 10 most used tools* for the EDAM operation: RNA-Seq analysis <br>
*based on usage statistics from Galaxy’s main servers over the last five years'
content:
- title_md: deseq2
description_md: |-
Differential gene expression analysis based on the negative binomial distribution
(Tool usage: 449489)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=deseq2">deseq2</a></li>
</ul>
- title_md: deg_annotate
description_md: |-
Annotate DESeq2/DEXSeq output tables
(Tool usage: 79388)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=deg_annotate">deg_annotate</a></li>
</ul>
- title_md: crosscontamination_barcode_filter
description_md: |-
Barcode contamination discovery tool
(Tool usage: 559)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=crosscontamination_barcode_filter">crosscontamination_barcode_filter</a></li>
</ul>
- title_md: velocyto
description_md: |-
Velocyto is a library for the analysis of RNA velocity.
(Tool usage: 398)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=velocyto_cli">velocyto_cli</a></li>
</ul>
- id: visualisation
title: Visualisation
heading_md: 'Top 10 most used tools* for the EDAM operation: Visualisation <br>
*based on usage statistics from Galaxy’s main servers over the last five years'
content:
- title_md: schicexplorer
description_md: |-
scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.
(Tool usage: 2204)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicadjustmatrix">schicexplorer_schicadjustmatrix</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccluster">schicexplorer_schiccluster</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclustercompartments">schicexplorer_schicclustercompartments</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclusterminhash">schicexplorer_schicclusterminhash</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclustersvl">schicexplorer_schicclustersvl</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicconsensusmatrices">schicexplorer_schicconsensusmatrices</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccorrectmatrices">schicexplorer_schiccorrectmatrices</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccreatebulkmatrix">schicexplorer_schiccreatebulkmatrix</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicdemultiplex">schicexplorer_schicdemultiplex</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicinfo">schicexplorer_schicinfo</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicmergematrixbins">schicexplorer_schicmergematrixbins</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicmergetoscool">schicexplorer_schicmergetoscool</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicnormalize">schicexplorer_schicnormalize</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicplotclusterprofiles">schicexplorer_schicplotclusterprofiles</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicplotconsensusmatrices">schicexplorer_schicplotconsensusmatrices</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicqualitycontrol">schicexplorer_schicqualitycontrol</a></li>
</ul>
- title_md: scpipe
description_md: |-
A flexible preprocessing pipeline for single-cell RNA-sequencing data
(Tool usage: 1443)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=scpipe">scpipe</a></li>
</ul>
- title_md: spapros
description_md: |-
Select and evaluate probe sets for targeted spatial transcriptomics.
(Tool usage: 3)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=spapros_evaluation">spapros_evaluation</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=spapros_selection">spapros_selection</a></li>
</ul>
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