diff --git a/communities/microgalaxy/lab/CONTRIBUTORS b/communities/microgalaxy/lab/CONTRIBUTORS index f1d71278..f26526af 100644 --- a/communities/microgalaxy/lab/CONTRIBUTORS +++ b/communities/microgalaxy/lab/CONTRIBUTORS @@ -1,3 +1,4 @@ # If GitHub username, name and avatar will be fetched and displayed bebatut -zierep \ No newline at end of file +zierep +EngyNasr \ No newline at end of file diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index f48401be..03d55058 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -1,5 +1,5 @@ # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/base.yml +# 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: @@ -7,37 +7,33 @@ # 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: Australia +site_name: European lab_name: microGalaxy Lab analysis_name: microGalaxy -nationality: Australian +nationality: European # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell -root_domain: usegalaxy.org +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 +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: Single Cell help forum - url: https://help.galaxyproject.org/tag/single-cell - 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: Single cell Slack channel (#single-cell-users) - url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7 - - title: Single cell user community chat room (Same channel but using Matrix/Element) - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - 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 @@ -49,7 +45,7 @@ conclusion_extra_md: "" # ----------------------------------------------------------------------------- # Custom content relative to this file URL -header_logo: static/logo_single_cell.svg +header_logo: static/microgalaxy-logo.png custom_css: static/custom.css intro_md: templates/intro.html conclusion_md: templates/conclusion.html @@ -61,9 +57,12 @@ footer_md: templates/footer.html # 1. Relative to this file URL # 2. Full URL to fetch globally centralized content sections: - - sections/1_beginner.yml - - sections/3_advanced.yml - - sections/4_community.yml - - sections/5_tools.yml + - 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 # ----------------------------------------------------------------------------- diff --git a/communities/microgalaxy/lab/sections/1_beginner.yml b/communities/microgalaxy/lab/sections/1_beginner.yml deleted file mode 100644 index d4aac6a8..00000000 --- a/communities/microgalaxy/lab/sections/1_beginner.yml +++ /dev/null @@ -1,233 +0,0 @@ -id: beginner -title: Learn to use Galaxy for microbial data analysis -tabs: - - id: learning_pathway - title: Learning pathways - heading_md: > - Connected tutorials to train you to perform single-cell analysis fast! - content: - - title_md: Introduction to Galaxy and Sequence analysis - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. 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. - - New to Galaxy and/or the field of genomics? Follow this {gtn modal}[learning path to get familiar with the basics](https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html)! - button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Genome annotation for prokaryotes - description_md: > - Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. - Check out the {gtn modal}[Genome annotation for prokaryotes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Detection of AMR genes in bacterial genomes - description_md: > - This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. - - Check out the {gtn modal}[Detection of AMR genes in bacterial genomes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Metagenomics data processing and analysis for microbiome - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications - - Check out the {gtn modal}[Metagenomics data processing and analysis for microbiome learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html - button_tip: Go to learning pathway - button_icon: tutorial - - title_md: Clinical metaproteomics workflows within Galaxy - description_md: > - This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis. - - Check out the {gtn modal}[Clinical metaproteomics workflows within Galaxy learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html - button_tip: View training menu - button_icon: tutorial - - - id: bacterial_genomics_tutorial - title: Bacterial genomics tutorials - heading_md: > - Using public data is free! Learn how to retrieve data from common sources. - content: - - title_md: Importing files from the Single Cell Expression Atlas - description_md: > - You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix! - EBI SCXA Data Retrieval - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa" - button_icon: run - button_tip: Run tool - - title_md: Importing from public atlases - Tutorial - description_md: > - You can learn more by following our dedicated to tutorial for importing files from public atlases. - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/tutorial.html - button_icon: tutorial - button_tip: View tutorial - - title_md: Importing from NCBI/GEO - description_md: > - Where there isn't a specific tool for retrieving data, you can nevertheless import and reformat data from the commonly used NCBI/GEO repository with the following tutorial. - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html - button_icon: tutorial - button_tip: View tutorial - - title_md: Importing 10X Files - description_md: > - You can find many tools for importing 10X formatted data into target datatypes. - Scanpy Read10x - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x" - button_icon: run - button_tip: Run tool - - title_md: Seurat Read10x - description_md: > - Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x" - button_icon: run - button_tip: Run tool - - title_md: DropletUtils Read10x - description_md: > - DropletUtils provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x" - button_icon: run - button_tip: Run tool - - - id: data_convert - title: Converting datatypes - heading_md: > - Single-cell data comes in many formats. - Here we show a few key tools in Galaxy for converting and manipulating objects in Galaxy. - content: - - title_md: SCEasy Converter - description_md: > - This tool allows you to convert between the following formats: - - - `hdf5` (AnnData/Loom) - - `rds` (Seurat) - - `rdata.sce` (Single Cell Experiment) - - `h5` (Seurat) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert" - button_icon: run - button_tip: Run tool - - title_md: Manipulate AnnData - description_md: > - Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as: - - - `Concatenate along the observations axis` for combining AnnData objects together - - `Transpose the data matrix` for help with converting formats - - `Filter observations or variables` for refining or subsetting your dataset - - `Adding annotations` and `Rename categories` for manipulating metadata - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate" - button_icon: run - button_tip: Run tool - - title_md: AnnData Operations - description_md: > - This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops" - button_icon: run - button_tip: Run tool - - title_md: Data conversion training - description_md: > - You can also explore our dedicated tutorial on single-cell data conversion. - button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" - button_icon: tutorial - button_tip: View tutorial - - - id: data_viz - title: Visualising Data - heading_md: > - There are a few key tools for visualising single-cell data in Galaxy. - content: - - title_md: Plot with Scanpy - description_md: > - This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot" - button_icon: run - button_tip: Run tool - - title_md: Scanpy PlotEmbed - description_md: > - This tool allows you to plot embeddings like UMAPs. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed" - button_icon: run - button_tip: Run tool - - title_md: Scanpy PlotTrajectory - description_md: > - This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory" - button_icon: run - button_tip: Run tool - - title_md: Scanpy Plot dimension reduction - description_md: > - This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. - inputs: - - label: Single cell data - datatypes: - - rds (Seurat object) - - rdata.sce (Single Cell Experiment) - - h5 (Seurat) - - hdf5 (Loom/AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot" - button_icon: run - button_tip: Run tool - - title_md: Plot with Seurat - description_md: > - This tool allows you to plot gene expressions, such as with Violin Plots. - inputs: - - label: Single cell data - datatypes: - - rds (Seurat object) - - rdata.sce (Single Cell Experiment) - - h5 (Seurat) - - hdf5 (Loom/AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot" - button_icon: run - button_tip: Run tool - - - id: help - title: Help - content: - - title_md: Single Cell help forum - description_md: > - Of course! Check out the Galaxy Project - [Single cell help forum](https://help.galaxyproject.org/tag/scrna) - - title_md: Troubleshooting errors - description_md: > - Find specific advice for - {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) - on the GTN. - - title_md: Can I upload sensitive data? - description_md: > - No, please do not upload personal or sensitive, such as human health or clinical data. Please see our - [Privacy Policy]({{ data_policy_url }}) - page for definitions of sensitive and health-related information. - - Please also make sure you have read our - [Terms of Service]({{ terms_url }}), - which covers hosting and analysis of research data. - - title_md: Is my data private? - description_md: > - Please read our - [Privacy Policy]({{ data_policy_url }}) - for information on your personal data and any data that you upload. - - title_md: How can I increase my storage quota? - description_md: > - 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. - button_md: Request - button_link: "{{ quota_request_url }}" - exclude_from: - - usegalaxy.org - - title_md: Galaxy {{ site_name }} support - description_md: > - Any user of Galaxy {{ site_name }} can request support online! - button_md: Request support - button_link: "{{ support_url }}" diff --git a/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml b/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml new file mode 100644 index 00000000..0c892cde --- /dev/null +++ b/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml @@ -0,0 +1,110 @@ +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: FastQC - sequence quality reports + description_md: > +

+ Before using your sequencing data, it's important to ensure that + the data quality is sufficient for your analysis. +

+ 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: FastP - sequence quality reports, trimming & filtering + description_md: > +

+ Faster run than FastQC, this tool can also trim reads and filter by quality. +

+ inputs: + - datatypes: + - fastq + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp" + - title_md: NanoPlot - visualize Oxford Nanopore data + description_md: > +

+ A plotting suite for Oxford Nanopore sequencing data and alignments. +

+ 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: GenomeScope - estimate genome size + description_md: > +

+ A set of metrics and graphs to visualize genome size and complexity prior to assembly. +

+ inputs: + - datatypes: + - tabular + label: Output from Meryl or Jellyfish histo + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope" + - title_md: Meryl - count kmers + description_md: > +

+ Prepare kmer count histogram for input to GenomeScope. +

+ 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. + Learn more. + content: + - title_md: Data QC + description_md: > +

+ Report statistics from sequencing reads.

Tools: nanoplot fastqc multiqc +

+ 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: > +

+ Estimates genome size and heterozygosity based on counts of kmers.

Tools: meryl genomescope +

+ 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: > +

+ Trims and filters raw sequence reads according to specified settings.

Tools: fastp +

+ 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: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/2_intermediate.yml b/communities/microgalaxy/lab/sections/2_intermediate.yml deleted file mode 100644 index f9cc27ae..00000000 --- a/communities/microgalaxy/lab/sections/2_intermediate.yml +++ /dev/null @@ -1,36 +0,0 @@ -id: intermediate -title: Advanced analysis -tabs: - - id: workflows - title: Multiomic Analyses - content: - - title_md: These tutorials use different methods to analyse scRNA-seq samples. - description_md: > - {gtn modal}[Learn more](https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/) - - - - - id: deconvolution - title: Deconvolution - heading_md: > - These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference - These tutorials use different methods to analyse scRNA-seq samples. - Learn more. - content: [] - - - id: tips - title: Tips, tricks & other hints - heading_md: > - These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference - These tutorials use different methods to analyse scRNA-seq samples. - Learn more. - content: - - title_md: About these workflows - description_md: > - Hello! Mehmet working here - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html#tip-creating-a-new-history - button_tip: View tutorial - button_icon: tutorial - - title_md: Spare space for another GTN - description_md: > - More GTN diff --git a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml new file mode 100644 index 00000000..f6cc84cd --- /dev/null +++ b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml @@ -0,0 +1,38 @@ +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: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/3_microbiome.yml b/communities/microgalaxy/lab/sections/3_microbiome.yml new file mode 100644 index 00000000..5e339542 --- /dev/null +++ b/communities/microgalaxy/lab/sections/3_microbiome.yml @@ -0,0 +1,38 @@ +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: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/4_community.yml b/communities/microgalaxy/lab/sections/4_community.yml deleted file mode 100644 index 16349ee3..00000000 --- a/communities/microgalaxy/lab/sections/4_community.yml +++ /dev/null @@ -1,31 +0,0 @@ -id: community -title: Community -tabs: - - id: participate - title: Participate - content: - - title_md: Chat with other users - description_md: > - Check out some suggestions on how you can - {gtn modal}[connect with the community](https://training.galaxyproject.org/training-material/topics/single-cell/faqs/user_community_join.html). - - title_md: Join our community! - description_md: > - - This Galaxy space is the result of hard, collaborative work by many contributors . - - It is maintained by the [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/). - - This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make single-cell & spatial omics analysis easier. - - Check out our site and join our community! - - button_link: "https://galaxyproject.org/community/sig/singlecell/" - button_md: 🖖🏽 - button_tip: Visit SPOC - - id: governance - title: How is the Galaxy Community organised? - content: - heading_md: > - Learn about the - {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN. - content: [] diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/4_tools.yml similarity index 100% rename from communities/microgalaxy/lab/sections/5_tools.yml rename to communities/microgalaxy/lab/sections/4_tools.yml diff --git a/communities/microgalaxy/lab/sections/3_advanced.yml b/communities/microgalaxy/lab/sections/5_workflows.yml similarity index 99% rename from communities/microgalaxy/lab/sections/3_advanced.yml rename to communities/microgalaxy/lab/sections/5_workflows.yml index bf837dac..b13d1053 100644 --- a/communities/microgalaxy/lab/sections/3_advanced.yml +++ b/communities/microgalaxy/lab/sections/5_workflows.yml @@ -1,4 +1,4 @@ -id: advanced +id: workflows title: Workflows tabs: - id: workflows1 @@ -49,6 +49,7 @@ tabs: button_link: "https://workflowhub.eu/search?q=microgalaxy+galaxy" button_md: 🔗 button_tip: Visit WorkflowHub + - id: workflows3 title: Community workflows heading_md: > diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml new file mode 100644 index 00000000..cce7e489 --- /dev/null +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -0,0 +1,51 @@ +id: support +title: Support & Help +tabs: + - id: help + title: Help + heading_md: > + You can browse through workflows before that have been reviewed by scientists. + content: + - title_md: Troubleshooting errors + description_md: > + Find specific advice for + {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) + on the GTN. + - title_md: Galaxy [American/Australia/EU/France/..] Support + description_md: > + Any user of Galaxy [American/Australia/EU/France/..] can request support online! + button_md: Request support + button_link: "{{ support_url }}" + - title_md: microGalaxy support + description_md: > + Users of microGalaxy can submit any kind of bug report via the microGalaxy webserver + button_link: "{{ galaxy_base_url }}" + button_md: microGalaxy support + - title_md: microGalaxy chat room + description_md: > + Of course! Check out the microGalaxy Matrix channel + button_link: "{{ microgalaxy_matrix }}" + button_md: Matrix channel + - title_md: Can I upload sensitive data? + description_md: > + No, please do not upload personal or sensitive, such as human health or clinical data. Please see our + [Privacy Policy]({{ data_policy_url }}) + page for definitions of sensitive and health-related information. + + Please also make sure you have read our + [Terms of Service]({{ terms_url }}), + which covers hosting and analysis of research data. + - title_md: Is my data private? + description_md: > + Please read our + [Privacy Policy]({{ data_policy_url }}) + for information on your personal data and any data that you upload. + + - id: request + title: Request + content: + - title_md: How can I increase my storage quota? + description_md: > + 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. + button_md: Request + button_link: "{{ quota_request_url }}" diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml new file mode 100644 index 00000000..ed3cc8ca --- /dev/null +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -0,0 +1,74 @@ +id: community +title: Community +tabs: + - id: participate + title: Participate + content: + - title_md: Chat with other users + description_md: > + Of course! Check out the microGalaxy Matrix channel + - title_md: Join our community! + description_md: > + + This Galaxy space is the result of hard, collaborative work by many contributors . + + It is maintained by the microGalaxy Community of Practice. + + This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier. + + Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)! + + button_link: "{{ microgalaxy_matrix }}" + button_md: + button_tip: Visit microGalaxy + + - id: governance + title: How is the Galaxy Community organised? + heading_md: > + Learn about the + {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN. + content: [] + + - id: links + title: Galaxy Community support links + content: + - title_md: General support + description_md: > + General Galaxy support + button_link: "{{ support_url }}" + button_md: Request support + - title_md: General help forum + description_md: > + General Galaxy help forum + button_link: "{{ galaxy_help_url }}" + button_md: Help forum + - title_md: Galaxy Training Network Slack workspace + description_md: > + GTN Slack channel + button_link: "{{ gtn_slack_url }}" + button_md: Slack channel + - title_md: Galaxy Training Network Community chat + description_md: > + GTN Matrix channel + button_link: "{{ gtn_matrix_channel }}" + button_md: Matrix channel + - title_md: microGalaxy user community chat room (Same channel but using Matrix/Element) + description_md: > + microGalaxy Matrix channel + button_link: "{{ microgalaxy_matrix }}" + button_md: Matrix channel + - title_md: American Galaxy Sever chat + description_md: > + Usegalaxy.org Matrix chat + button_link: "{{ american_server }}" + button_md: Matrix channel + - title_md: Australian Galaxy Server chat + description_md: > + Usegalaxy.org.au chat + button_link: "{{ australian_server }}" + button_md: Request form + - title_md: European Galaxy server chat + description_md: > + Usegalaxy.eu Matrix chat + button_link: "{{ european_server }}" + button_md: Matrix channel \ No newline at end of file diff --git a/communities/microgalaxy/lab/static/logo_single_cell.svg b/communities/microgalaxy/lab/static/logo_single_cell.svg deleted file mode 100644 index 43540c2b..00000000 --- a/communities/microgalaxy/lab/static/logo_single_cell.svg +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/communities/microgalaxy/lab/static/microgalaxy-logo.png b/communities/microgalaxy/lab/static/microgalaxy-logo.png new file mode 100644 index 00000000..ea12683d Binary files /dev/null and b/communities/microgalaxy/lab/static/microgalaxy-logo.png differ diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html index b751908f..fdfbc08a 100644 --- a/communities/microgalaxy/lab/templates/conclusion.html +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -1,8 +1,8 @@ {% load markdown %} -
+ {% if feedback_email %}
diff --git a/communities/microgalaxy/lab/usegalaxy.eu.yml b/communities/microgalaxy/lab/usegalaxy.eu.yml index 67143644..8343e551 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu.yml +++ b/communities/microgalaxy/lab/usegalaxy.eu.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.eu.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.eu.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: @@ -13,8 +13,8 @@ site_name: Europe nationality: European # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.eu -subdomain: singlecell +galaxy_base_url: https://microgalaxy.usegalaxy.eu +subdomain: microGalaxy root_domain: usegalaxy.eu # This will enable a feedback form on the webpage: @@ -25,14 +25,12 @@ data_policy_url: "#data-policy" terms_url: https://usegalaxy-eu.github.io/gdpr/tos.html help_links: - - title: Single Cell community help forum - url: https://help.galaxyproject.org/tag/scrna - title: General Galaxy support url: https://galaxyproject.org/support/ - title: Galaxy EU help forum url: https://help.galaxyproject.org/c/usegalaxy-eu-support/6 - - title: Single cell Galaxy user community chat room - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: microGalaxy Galaxy user community chat room + 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.eu chat diff --git a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html index 0ff9c101..f87a847b 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html +++ b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html @@ -42,7 +42,7 @@

- Edit this page on GitHub + Edit this page on GitHub   diff --git a/communities/microgalaxy/lab/usegalaxy.org.au.yml b/communities/microgalaxy/lab/usegalaxy.org.au.yml index 0a032cc7..fa7ccd02 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.au.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.au.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.au.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.org.au.yml # ----------------------------------------------------------------------------- # Use these variables in MD/HTML templates like: @@ -13,8 +13,8 @@ site_name: Australia nationality: Australian # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org.au -subdomain: singlecell +galaxy_base_url: https://microgalaxy.usegalaxy.org.au +subdomain: microGalaxy root_domain: usegalaxy.org.au # This will enable a feedback form on the webpage: @@ -31,12 +31,10 @@ help_links: url: https://site.usegalaxy.org.au/request - title: General Galaxy support url: https://galaxyproject.org/support/ - - title: Single Cell community help forum - url: https://usegalaxy-eu.github.io/scrna - title: General Galaxy help forum url: https://help.galaxyproject.org - - title: Single cell Galaxy user community chat room - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: microGalaxy Galaxy user community chat room + 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 diff --git a/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html index fa4d580e..1935fba9 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html +++ b/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html @@ -116,4 +116,4 @@

CONNECT
- + \ No newline at end of file diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml index 63934752..7ec421c2 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.org.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: @@ -13,22 +13,20 @@ site_name: "" # ? nationality: "" # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell +galaxy_base_url: https://microgalaxy.usegalaxy.org +subdomain: microGalaxy root_domain: usegalaxy.org # This will enable a feedback form on the webpage: # feedback_email: help@mygalaxy.org help_links: - - title: Single Cell community help forum - url: https://usegalaxy-eu.github.io/scrna - title: General Galaxy support url: https://galaxyproject.org/support/ - title: General Galaxy help forum url: https://help.galaxyproject.org - - title: Single cell Galaxy user community chat room - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: microGalaxy Galaxy user community chat room + 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