diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 38d40e0a..012bea3b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -64,7 +64,7 @@ jobs: bash sources/bin/get_community_tools.sh test - name: Create interactive table and wordcloud run: | - bash sources/bin/format_tools.sh + bash sources/bin/format_tools.sh test test-tutorials: runs-on: ubuntu-20.04 diff --git a/communities/microgalaxy/subdomain/CONTRIBUTORS b/communities/microgalaxy/subdomain/CONTRIBUTORS deleted file mode 100644 index 8f11c343..00000000 --- a/communities/microgalaxy/subdomain/CONTRIBUTORS +++ /dev/null @@ -1,29 +0,0 @@ -# If GitHub username, name and avatar will be fetched and displayed -neoformit -nomadscientist -GarethPrice-Aus -mtekman -pavanvidem -pcm32 -kysrpex -astrovsky01 -a-solovyev12 -bebatut -bgruening -cartal -cgirardot -drosofff -blankenberg -fidelram -ethering -hexylena -irenepapatheodo -jxtx -scholtalbers -pinin4fjords -ktpolanski -bellenger-l -mblue9 -nh3 -nsoranzo -suhaibMo diff --git a/communities/microgalaxy/subdomain/LICENSE b/communities/microgalaxy/subdomain/LICENSE deleted file mode 100644 index f84a6a6f..00000000 --- a/communities/microgalaxy/subdomain/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2024 Gareth Price - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/communities/microgalaxy/subdomain/README.md b/communities/microgalaxy/subdomain/README.md deleted file mode 100644 index 0105b125..00000000 --- a/communities/microgalaxy/subdomain/README.md +++ /dev/null @@ -1,2 +0,0 @@ -# microGalaxy subdomain/Lab - diff --git a/communities/microgalaxy/subdomain/base.yml b/communities/microgalaxy/subdomain/base.yml deleted file mode 100644 index d9fec4da..00000000 --- a/communities/microgalaxy/subdomain/base.yml +++ /dev/null @@ -1,68 +0,0 @@ -# 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 - -# ----------------------------------------------------------------------------- -# 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: Australia -lab_name: microGalaxy Lab -analysis_name: microGalaxy -nationality: Australian - -# Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell -root_domain: usegalaxy.org - -# 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: 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: 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/logo_single_cell.svg -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_beginner.yml - - sections/3_advanced.yml - - sections/4_community.yml - -# ----------------------------------------------------------------------------- diff --git a/communities/microgalaxy/subdomain/sections/1_beginner.yml b/communities/microgalaxy/subdomain/sections/1_beginner.yml deleted file mode 100644 index d4aac6a8..00000000 --- a/communities/microgalaxy/subdomain/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/subdomain/sections/2_intermediate.yml b/communities/microgalaxy/subdomain/sections/2_intermediate.yml deleted file mode 100644 index f9cc27ae..00000000 --- a/communities/microgalaxy/subdomain/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/subdomain/sections/3_advanced.yml b/communities/microgalaxy/subdomain/sections/3_advanced.yml deleted file mode 100644 index bf837dac..00000000 --- a/communities/microgalaxy/subdomain/sections/3_advanced.yml +++ /dev/null @@ -1,80 +0,0 @@ -id: advanced -title: Workflows -tabs: - - id: workflows1 - title: Workflow Best Practices - heading_md: > -
-

- Workflows are chains of of tools that can be run together at the click of a button. - The above tabs contain both peer reviewed and community submitted workflows. -

-

- Tag your workflows - with #microgalaxy and share publicly with other users! -

- Additional common workflow tags for our community are: - -
- - content: - - title_md: How to tag a workflow - description_md: > - - - title_md: WorkflowHub - description_md: > - WorkflowHub hosts high quality workflows. You can explore microGalaxy workflows from WorkflowHub. - button_link: "https://workflowhub.eu/search?q=microgalaxy+galaxy" - button_md: 🔗 - button_tip: Visit WorkflowHub - - id: workflows3 - title: Community workflows - heading_md: > - Anyone on Galaxy can share their workflow publicly - if your workflow is running well, share it with others! -

You can search these community workflows below.

- content: - - title_md: Community Workflows - description_md: > - Search through community workflows tagged with #microgalaxy. - - - - title_md: Advanced workflow search - description_md: > - The GTN's - {gtn modal}[Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list.html) - allows you to search for workflows across all of Galaxy! - - button_link: "https://training.galaxyproject.org/training-material/workflows/list.html" - button_md: 🔗 - button_tip: Visit WorkflowHub - - - title_md: How to share your workflow - description_md: > - Learn how to {gtn modal}[publish your workflow](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_publish.html) - to share your work with the Galaxy community. diff --git a/communities/microgalaxy/subdomain/sections/4_community.yml b/communities/microgalaxy/subdomain/sections/4_community.yml deleted file mode 100644 index 16349ee3..00000000 --- a/communities/microgalaxy/subdomain/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/subdomain/static/custom.css b/communities/microgalaxy/subdomain/static/custom.css deleted file mode 100644 index e69de29b..00000000 diff --git a/communities/microgalaxy/subdomain/static/logo_single_cell.svg b/communities/microgalaxy/subdomain/static/logo_single_cell.svg deleted file mode 100644 index 43540c2b..00000000 --- a/communities/microgalaxy/subdomain/static/logo_single_cell.svg +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/communities/microgalaxy/subdomain/templates/conclusion.html b/communities/microgalaxy/subdomain/templates/conclusion.html deleted file mode 100644 index b751908f..00000000 --- a/communities/microgalaxy/subdomain/templates/conclusion.html +++ /dev/null @@ -1,45 +0,0 @@ -{% load markdown %} - -
- {% if help_links %} -

Single Cell and Spatial Omics community support

- - {% endif %} -
- -
-

News and Events

- -
-
- -
-
- -
-
-
- -{% if feedback_email %} -
-

What do you think of the {{ lab_name }}?

- -
-{% endif %} - - -
- {{ conclusion_extra_md|safe }} -
diff --git a/communities/microgalaxy/subdomain/templates/footer.html b/communities/microgalaxy/subdomain/templates/footer.html deleted file mode 100644 index e69de29b..00000000 diff --git a/communities/microgalaxy/subdomain/templates/intro.html b/communities/microgalaxy/subdomain/templates/intro.html deleted file mode 100644 index 625c1d4d..00000000 --- a/communities/microgalaxy/subdomain/templates/intro.html +++ /dev/null @@ -1,45 +0,0 @@ -
-

- Welcome to the Galaxy {{ site_name }} {{ lab_name }}! -

- -

- Whether you are analysing microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics, transcriptomics, proteomics or metabolomics, multiomics or integrative analysis this is the place to be! -

-

- - How does this page relate to Galaxy {{ site_name }}? - -

- - {{ intro_extra_md }} - - -
diff --git a/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml b/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml deleted file mode 100644 index 30e12240..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: HCA-Scanpy -tools: -- name: seurat_plot - owner: ebi-gxa -- name: scanpy_integrate_bbknn - owner: ebi-gxa -- name: scanpy_integrate_combat - owner: ebi-gxa -- name: scanpy_integrate_mnn - owner: ebi-gxa -- name: scanpy_plot_scrublet - owner: ebi-gxa -- name: scanpy_multiplet_scrublet - owner: ebi-gxa -- name: seurat_run_umap - owner: ebi-gxa diff --git a/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml.lock b/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml.lock deleted file mode 100644 index 62bc2659..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/hca-scanpy.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: HCA-Scanpy -tools: -- name: seurat_plot - owner: ebi-gxa - revisions: - - 95d79f1134f0 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: scanpy_integrate_bbknn - owner: ebi-gxa - revisions: - - c9da9192eee5 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: scanpy_integrate_combat - owner: ebi-gxa - revisions: - - 3c47bc560688 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: scanpy_integrate_mnn - owner: ebi-gxa - revisions: - - ff6decc0f432 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: scanpy_plot_scrublet - owner: ebi-gxa - revisions: - - 6f5509cf3176 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: scanpy_multiplet_scrublet - owner: ebi-gxa - revisions: - - 53ce0e336840 - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy -- name: seurat_run_umap - owner: ebi-gxa - revisions: - - b9424c715a0d - tool_panel_section_id: hca_scanpy - tool_panel_section_label: HCA-Scanpy diff --git a/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml b/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml deleted file mode 100644 index 7c94a0de..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml +++ /dev/null @@ -1,120 +0,0 @@ -tool_panel_section_label: HiCExplorer -tools: -- name: hicexplorer_chicaggregatestatistic - owner: bgruening -- name: hicexplorer_chicdifferentialtest - owner: bgruening -- name: hicexplorer_chicexportdata - owner: bgruening -- name: hicexplorer_chicplotviewpoint - owner: bgruening -- name: hicexplorer_chicqualitycontrol - owner: bgruening -- name: hicexplorer_chicsignificantinteractions - owner: bgruening -- name: hicexplorer_chicviewpoint - owner: bgruening -- name: hicexplorer_chicqualitycontrol - owner: bgruening -- name: hicexplorer_chicsignificantinteractions - owner: bgruening -- name: hicexplorer_chicviewpoint - owner: bgruening -- name: hicexplorer_chicviewpointbackgroundmodel - owner: bgruening -- name: hicexplorer_hicadjustmatrix - owner: bgruening -- name: hicexplorer_hicaggregatecontacts - owner: bgruening -- name: hicexplorer_hicaverageregions - owner: bgruening -- name: hicexplorer_hicbuildmatrix - owner: bgruening -- name: hicexplorer_hiccomparematrices - owner: bgruening -- name: hicexplorer_hiccompartmentspolarization - owner: bgruening -- name: hicexplorer_hicconvertformat - owner: bgruening -- name: hicexplorer_hiccorrectmatrix - owner: bgruening -- name: hicexplorer_hiccorrelate - owner: bgruening -- name: hicexplorer_hicdetectloops - owner: bgruening -- name: hicexplorer_hicdifferentialtad - owner: bgruening -- name: hicexplorer_hicfindrestrictionsites - owner: bgruening -- name: hicexplorer_hicfindtads - owner: bgruening -- name: hicexplorer_hichyperoptdetectloops - owner: bgruening -- name: hicexplorer_hicinfo - owner: bgruening -- name: hicexplorer_hicinterintratad - owner: bgruening -- name: hicexplorer_hicmergedomains - owner: bgruening -- name: hicexplorer_hicmergeloops - owner: bgruening -- name: hicexplorer_hicmergematrixbins - owner: bgruening -- name: hicexplorer_hicnormalize - owner: bgruening -- name: hicexplorer_hicpca - owner: bgruening -- name: hicexplorer_hicplotaverageregions - owner: bgruening -- name: hicexplorer_hicplotdistvscounts - owner: bgruening -- name: hicexplorer_hicplotmatrix - owner: bgruening -- name: hicexplorer_hicplotsvl - owner: bgruening -- name: hicexplorer_hicplotviewpoint - owner: bgruening -- name: hicexplorer_hicquickqc - owner: bgruening -- name: hicexplorer_hicsummatrices - owner: bgruening -- name: hicexplorer_hictadclassifier - owner: bgruening -- name: hicexplorer_hictraintadclassifier - owner: bgruening -- name: hicexplorer_hictransform - owner: bgruening -- name: hicexplorer_hicvalidatelocations - owner: bgruening -- name: schicexplorer_schicadjustmatrix - owner: iuc -- name: schicexplorer_schiccluster - owner: iuc -- name: schicexplorer_schicclustercompartments - owner: iuc -- name: schicexplorer_schicclusterminhash - owner: iuc -- name: schicexplorer_schicclustersvl - owner: iuc -- name: schicexplorer_schicconsensusmatrices - owner: iuc -- name: schicexplorer_schiccorrectmatrices - owner: iuc -- name: schicexplorer_schiccreatebulkmatrix - owner: iuc -- name: schicexplorer_schicdemultiplex - owner: iuc -- name: schicexplorer_schicinfo - owner: iuc -- name: schicexplorer_schicmergematrixbins - owner: iuc -- name: schicexplorer_schicmergetoscool - owner: iuc -- name: schicexplorer_schicnormalize - owner: iuc -- name: schicexplorer_schicplotclusterprofiles - owner: iuc -- name: schicexplorer_schicplotconsensusmatrices - owner: iuc -- name: schicexplorer_schicqualitycontrol - owner: iuc diff --git a/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml.lock b/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml.lock deleted file mode 100644 index a86a55c1..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/hicexplorer.yml.lock +++ /dev/null @@ -1,359 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: HiCExplorer -tools: -- name: hicexplorer_chicaggregatestatistic - owner: bgruening - revisions: - - 01c37e54e86e - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicdifferentialtest - owner: bgruening - revisions: - - 9d42a6133690 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicexportdata - owner: bgruening - revisions: - - 23b8d6b8960c - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicplotviewpoint - owner: bgruening - revisions: - - 013e53ccc7ac - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicqualitycontrol - owner: bgruening - revisions: - - b892fa1fcaec - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicsignificantinteractions - owner: bgruening - revisions: - - 640e0e45518a - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_chicviewpoint - owner: bgruening - 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tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicinfo - owner: bgruening - revisions: - - e4f8fceab96a - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicinterintratad - owner: bgruening - revisions: - - 55b013e59018 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicmergedomains - owner: bgruening - revisions: - - b376ef118807 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicmergeloops - owner: bgruening - revisions: - - 1511a8ebe906 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicmergematrixbins - owner: bgruening - revisions: - - 977dc15add20 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicnormalize - owner: bgruening - revisions: - - 6d042c96aceb - tool_panel_section_id: hicexplorer - 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tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schiccreatebulkmatrix - owner: iuc - revisions: - - acb3ed49109e - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicdemultiplex - owner: iuc - revisions: - - f224fc9af1d3 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicinfo - owner: iuc - revisions: - - 41b415c410e3 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicmergematrixbins - owner: iuc - revisions: - - 47ef02546fe9 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicmergetoscool - owner: iuc - revisions: - - 70a13d0a950f - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicnormalize - owner: iuc - revisions: - - 66e96c3d3c5d - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicplotclusterprofiles - owner: iuc - revisions: - - 65f2f5d29947 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicplotconsensusmatrices - owner: iuc - revisions: - - 95b1216e1e70 - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer -- name: schicexplorer_schicqualitycontrol - owner: iuc - revisions: - - 4a841ab67e3b - tool_panel_section_id: hicexplorer - tool_panel_section_label: HiCExplorer diff --git a/communities/microgalaxy/subdomain/tool_panel/import.yml b/communities/microgalaxy/subdomain/tool_panel/import.yml deleted file mode 100644 index f87138d9..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/import.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Import/manipulate sc data -tools: -- name: 10x_bamtofastq - owner: bgruening -- name: scater_read_10x_results - owner: ebi-gxa -- name: gsc_scran_normalize - owner: artbio diff --git a/communities/microgalaxy/subdomain/tool_panel/import.yml.lock b/communities/microgalaxy/subdomain/tool_panel/import.yml.lock deleted file mode 100644 index 8b5f8cd3..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/import.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: Import/manipulate sc data -tools: -- name: 10x_bamtofastq - owner: bgruening - revisions: - - f71fd828c126 - tool_panel_section_id: import_manipulate_sc_data - tool_panel_section_label: Import/manipulate sc data -- name: scater_read_10x_results - owner: ebi-gxa - revisions: - - da3f394039b5 - tool_panel_section_id: import_manipulate_sc_data - tool_panel_section_label: Import/manipulate sc data -- name: gsc_scran_normalize - owner: artbio - revisions: - - 6864acb21714 - tool_panel_section_id: import_manipulate_sc_data - tool_panel_section_label: Import/manipulate sc data diff --git a/communities/microgalaxy/subdomain/tool_panel/multiomics.yml b/communities/microgalaxy/subdomain/tool_panel/multiomics.yml deleted file mode 100644 index e305aae5..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/multiomics.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Multiomics -tools: -- name: episcanpy_cluster_embed - owner: iuc diff --git a/communities/microgalaxy/subdomain/tool_panel/multiomics.yml.lock b/communities/microgalaxy/subdomain/tool_panel/multiomics.yml.lock deleted file mode 100644 index 467ea6c6..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/multiomics.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: Multiomics -tools: -- name: episcanpy_cluster_embed - owner: iuc - revisions: - - f4713992f23a - tool_panel_section_id: multiomics - tool_panel_section_label: Multiomics diff --git a/communities/microgalaxy/subdomain/tool_panel/sccaf.yml b/communities/microgalaxy/subdomain/tool_panel/sccaf.yml deleted file mode 100644 index 45909169..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/sccaf.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: SCCAF -tools: -- name: run_sccaf - owner: ebi-gxa -- name: sccaf_asses - owner: ebi-gxa -- name: sccaf_asses_merger - owner: ebi-gxa -- name: sccaf_regress_out - owner: ebi-gxa diff --git a/communities/microgalaxy/subdomain/tool_panel/sccaf.yml.lock b/communities/microgalaxy/subdomain/tool_panel/sccaf.yml.lock deleted file mode 100644 index 49c80525..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/sccaf.yml.lock +++ /dev/null @@ -1,29 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: SCCAF -tools: -- name: run_sccaf - owner: ebi-gxa - revisions: - - 647d34f125bc - tool_panel_section_id: sccaf - tool_panel_section_label: SCCAF -- name: sccaf_asses - owner: ebi-gxa - revisions: - - 37a4c22f600b - tool_panel_section_id: sccaf - tool_panel_section_label: SCCAF -- name: sccaf_asses_merger - owner: ebi-gxa - revisions: - - 99d15ded4d5f - tool_panel_section_id: sccaf - tool_panel_section_label: SCCAF -- name: sccaf_regress_out - owner: ebi-gxa - revisions: - - 5ef0610e9f50 - tool_panel_section_id: sccaf - tool_panel_section_label: SCCAF diff --git a/communities/microgalaxy/subdomain/tool_panel/seurat.yml b/communities/microgalaxy/subdomain/tool_panel/seurat.yml deleted file mode 100644 index 0b95e939..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/seurat.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Seurat -tools: -- name: seurat_create_seurat_object - owner: ebi-gxa -- name: seurat_export_cellbrowser - owner: ebi-gxa -- name: seurat_filter_cells - owner: ebi-gxa -- name: seurat_find_clusters - owner: ebi-gxa -- name: seurat_find_markers - owner: ebi-gxa -- name: seurat_find_neighbours - owner: ebi-gxa -- name: seurat_find_variable_genes - owner: ebi-gxa -- name: seurat_normalise_data - owner: ebi-gxa -- name: seurat_dim_plot - owner: ebi-gxa -- name: seurat_read10x - owner: ebi-gxa -- name: seurat_run_pca - owner: ebi-gxa -- name: seurat_run_tsne - owner: ebi-gxa -- name: seurat_scale_data - owner: ebi-gxa diff --git a/communities/microgalaxy/subdomain/tool_panel/seurat.yml.lock b/communities/microgalaxy/subdomain/tool_panel/seurat.yml.lock deleted file mode 100644 index cf910f55..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/seurat.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: Seurat -tools: -- name: seurat_create_seurat_object - owner: ebi-gxa - revisions: - - f8865ae30723 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_export_cellbrowser - owner: ebi-gxa - revisions: - - 36221da750e8 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_filter_cells - owner: ebi-gxa - revisions: - - cd9f564bd63f - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_find_clusters - owner: ebi-gxa - revisions: - - d541e9e62beb - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_find_markers - owner: ebi-gxa - revisions: - - 07fc9f4841b3 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_find_neighbours - owner: ebi-gxa - revisions: - - ba897c57bdd9 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_find_variable_genes - owner: ebi-gxa - revisions: - - 948fc0276b4f - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_normalise_data - owner: ebi-gxa - revisions: - - 3f49bc9c9213 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_dim_plot - owner: ebi-gxa - revisions: - - 64174ac50d78 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_read10x - owner: ebi-gxa - revisions: - - f5db0e853f57 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_run_pca - owner: ebi-gxa - revisions: - - 8ded486b0014 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_run_tsne - owner: ebi-gxa - revisions: - - 0db997e4a81d - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_scale_data - owner: ebi-gxa - revisions: - - 5e9ba303f9e1 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat diff --git a/communities/microgalaxy/subdomain/tool_panel/single_cell.yml b/communities/microgalaxy/subdomain/tool_panel/single_cell.yml deleted file mode 100644 index a8a11fed..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/single_cell.yml +++ /dev/null @@ -1,136 +0,0 @@ -tool_panel_section_label: Single-cell -tools: -- name: scanpy_plot - owner: iuc -- name: scanpy_inspect - owner: iuc -- name: scanpy_filter - owner: iuc -- name: scanpy_normalize - owner: iuc -- name: scanpy_cluster_reduce_dimension - owner: iuc -- name: scanpy_remove_confounders - owner: iuc -- name: anndata_export - owner: iuc -- name: anndata_import - owner: iuc -- name: anndata_inspect - owner: iuc -- name: anndata_manipulate - owner: iuc -- name: modify_loom - owner: iuc -- name: dropletutils - owner: iuc -- name: raceid_clustering - owner: iuc -- name: raceid_filtnormconf - owner: iuc -- name: raceid_inspectclusters - owner: iuc -- name: raceid_inspecttrajectory - owner: iuc -- name: raceid_trajectory - owner: iuc -- name: scanpy_filter_cells - owner: ebi-gxa -- name: scanpy_filter_genes - owner: ebi-gxa -- name: scanpy_normalise_data - owner: ebi-gxa -- name: scanpy_find_variable_genes - owner: ebi-gxa -- name: scanpy_scale_data - owner: ebi-gxa -- name: scanpy_run_pca - owner: ebi-gxa -- name: scanpy_compute_graph - owner: ebi-gxa -- name: scanpy_run_tsne - owner: ebi-gxa -- name: scanpy_run_umap - owner: ebi-gxa -- name: scanpy_find_cluster - owner: ebi-gxa -- name: scanpy_find_markers - owner: ebi-gxa -- name: scanpy_plot_embed - owner: ebi-gxa -- name: anndata_ops - owner: ebi-gxa -- name: scanpy_parameter_iterator - owner: ebi-gxa -- name: scanpy_read_10x - owner: ebi-gxa -- name: scanpy_integrate_harmony - owner: ebi-gxa -- name: gtf2gene_list - owner: ebi-gxa -- name: scanpy_run_fdg - owner: ebi-gxa -- name: scanpy_run_diffmap - owner: ebi-gxa -- name: scanpy_run_paga - owner: ebi-gxa -- name: scanpy_run_dpt - owner: ebi-gxa -- name: scanpy_plot_trajectory - owner: ebi-gxa -- name: alevin - owner: bgruening -- name: droplet_barcode_plot - owner: ebi-gxa -- name: salmon_kallisto_mtx_to_10x - owner: ebi-gxa -- name: dropletutils_read_10x - owner: ebi-gxa -- name: dropletutils_empty_drops - owner: ebi-gxa -- name: sceasy_convert - owner: ebi-gxa -- name: retrieve_scxa - owner: ebi-gxa -- name: scanpy_regress_variable - owner: ebi-gxa -- name: music_construct_eset - owner: bgruening -- name: music_inspect_eset - owner: bgruening -- name: music_manipulate_eset - owner: bgruening -- name: music_deconvolution - owner: bgruening -- name: music_compare - owner: bgruening -- name: episcanpy_build_matrix - owner: iuc -- name: episcanpy_preprocess - owner: iuc -- name: sinto_barcode - owner: iuc -- name: sinto_fragments - owner: iuc -- name: baredsc_1d - owner: iuc -- name: baredsc_2d - owner: iuc -- name: baredsc_combine_1d - owner: iuc -- name: baredsc_combine_2d - owner: iuc -- name: cite_seq_count - owner: iuc -- name: velocyto_cli - owner: iuc -- name: gsc_scran_normalize - owner: artbio -- name: snapatac2_clustering - owner: iuc -- name: snapatac2_peaks_and_motif - owner: iuc -- name: snapatac2_plotting - owner: iuc -- name: snapatac2_preprocessing - owner: iuc diff --git a/communities/microgalaxy/subdomain/tool_panel/single_cell.yml.lock b/communities/microgalaxy/subdomain/tool_panel/single_cell.yml.lock deleted file mode 100644 index 7e805143..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/single_cell.yml.lock +++ /dev/null @@ -1,568 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: Single-cell -tools: -- name: scanpy_plot - owner: iuc - revisions: - - 6adf98e782f3 - - 6f5349dd5c49 - - 7647e5cd1b8b - - 95777145cb92 - - 9a169729c9f9 - - 9b0cdb8cf6be - - aa0c474463c2 - - f7446fd8d5e7 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_inspect - owner: iuc - revisions: - - 3081ff5c84a3 - - 5c3ebe2adc77 - - 6bd82ed14acd - - 6c145a6868cc - - 9d33775ec67d - - c5d3684f7c4c - - e4c99c83dfbf - - f54f0f0598ad - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_filter - owner: iuc - revisions: - - 277313130da5 - - 2d02d9702d3a - - 3c86f71498bc - - 5511647110ff - - a03ff8633507 - - b409c2486353 - - d636ce5cde16 - - f87ed6503715 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_normalize - owner: iuc - revisions: - - 51d945eab1e1 - - 5342ce58cd1e - - 7b9fafe32c86 - - 94c19fb1281c - - a407e7f8bdc1 - - ab55fe8030b6 - - c9cb76cf8d6c - - d844935c906c - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_cluster_reduce_dimension - owner: iuc - revisions: - - 35bc2eb568ed - - 3e4e1cf73d98 - - 4d8f983cd751 - - 6acb08931836 - - 6f83f8fd381f - - aaa5da8e73a9 - - b2df381a6004 - - edec35114f72 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_remove_confounders - owner: iuc - revisions: - - 215733a383f2 - - 458e8f43a775 - - 73ab2ac53d06 - - 80d4e2cac903 - - bf2017df9837 - - c2ef03559dc6 - - c65fce500915 - - d18e7a6e5cd4 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: anndata_export - owner: iuc - revisions: - - 0cb889db0910 - - 32c5c85cbc12 - - c0b037b12765 - - c5ac926c838f - - e1c3c2f2a834 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: anndata_import - owner: iuc - revisions: - - 00712416fdaa - - '499059586799' - - 93dd15e13e6a - - ae1e5d9d8972 - - cfc3f5a57dc6 - - fb9e030ffae4 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: anndata_inspect - owner: iuc - revisions: - 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revisions: - - 43c146e25a43 - - 7608d5faee41 - - b83fbc90161e - - d45f092caf24 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: raceid_inspectclusters - owner: iuc - revisions: - - 37a47c4fd84d - - 41f34e925bd5 - - be4646256624 - - f3eb2291da05 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: raceid_inspecttrajectory - owner: iuc - revisions: - - 3478133d0f6f - - 69018f285aa3 - - a6821f856a1e - - c8434a623268 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: raceid_trajectory - owner: iuc - revisions: - - 2af7c5086a96 - - 44b935f2271b - - 72979cac22b2 - - e93b008c637a - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_filter_cells - owner: ebi-gxa - revisions: - - 7fd39eb52f38 - - 8ed4e80e8799 - - ba64b91ed2b9 - - bf1e0bdec1db - - e9283529cba1 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_filter_genes - owner: ebi-gxa - revisions: - - 474a69c47184 - - 7143938df06e - - a1698b43abeb - - cc64914b0cf4 - - d82d999fa716 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_normalise_data - owner: ebi-gxa - revisions: - - 1e9616772e16 - - 3027cb62adbd - - 3a4564b9d685 - - 6b97ffba31da - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_find_variable_genes - owner: ebi-gxa - revisions: - - 2861ca3bfe4d - - 5c62f39aab8f - - 64dd8bb151e1 - - 82bd7bf93454 - - ae467daae2f7 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_scale_data - owner: ebi-gxa - revisions: - - 22f2957da902 - - 2b6913c840bf - - 4cc9362782b4 - - f86b2c3bc459 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_run_pca - owner: ebi-gxa - revisions: - - 04bdc69f00d7 - - 4428dba93375 - - 59028945c857 - - 988edd5fa902 - - c4f7fb2b1f70 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_compute_graph - owner: ebi-gxa - revisions: - - 22bd5861706d - - 3cf0177ed87e - - 5ec3b715809c - - 6417cccad133 - - fcaa9048cdaf - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_run_tsne - owner: ebi-gxa - revisions: - - 181d61d2f3cd - - 384cacc40611 - - a147dce191e9 - - abdb61e4afa3 - - fe727a9496ea - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_run_umap - owner: ebi-gxa - revisions: - - abae3d11d920 - - ad70b3552c99 - - bd4a244faeb8 - - e31937baa330 - - ea91cfd0444e - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_find_cluster - owner: ebi-gxa - revisions: - - 15e8a4c60418 - - 2ccd9f9e2cd0 - - 36735850e461 - - 621d7d7a605f - - 8dc3d8941217 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_find_markers - owner: ebi-gxa - revisions: - - 615a46c220f0 - - 7042ce140caa - 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tool_panel_section_label: Single-cell -- name: retrieve_scxa - owner: ebi-gxa - revisions: - - 72b6e1747e37 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_regress_variable - owner: ebi-gxa - revisions: - - 0bab2ae44e7a - - 1200b55768ce - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: music_construct_eset - owner: bgruening - revisions: - - 282819d09a4f - - 2cfd0db49bbc - - 7ffaa0968da3 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: music_inspect_eset - owner: bgruening - revisions: - - 7705cc75ac18 - - 8c64a2da3869 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: music_manipulate_eset - owner: bgruening - revisions: - - 22232092be53 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: music_deconvolution - owner: bgruening - revisions: - - 2ba99a52bd44 - - 56371b5a2da9 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: music_compare - owner: bgruening - revisions: - - 4447ed460308 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: episcanpy_build_matrix - owner: iuc - revisions: - - 31a21ba2c5ea - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: episcanpy_preprocess - owner: iuc - revisions: - - 29f5f25b9935 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: sinto_barcode - owner: iuc - revisions: - - d1b34ac42b8f - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: sinto_fragments - owner: iuc - revisions: - - 29e6bfb2cf49 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: baredsc_1d - owner: iuc - revisions: - - 02b1fe7aed76 - - 0e70b2dfe4be - - 4fff5a293013 - - 769d815e4b0d - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: baredsc_2d - owner: iuc - 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owner: iuc - revisions: - - 8f8bef61fd0b - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: snapatac2_peaks_and_motif - owner: iuc - revisions: - - 588c811fdd48 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: snapatac2_plotting - owner: iuc - revisions: - - fecf9664c885 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: snapatac2_preprocessing - owner: iuc - revisions: - - cec3e76eaf05 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell diff --git a/communities/microgalaxy/subdomain/tool_panel/spatial.yml b/communities/microgalaxy/subdomain/tool_panel/spatial.yml deleted file mode 100644 index 85d64f88..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/spatial.yml +++ /dev/null @@ -1,14 +0,0 @@ -tool_panel_section_label: Spatial -tools: -- name: quantification - owner: perssond -- name: cell_intensity_processing - owner: goeckslab -- name: s3segmenter - owner: perssond -- name: slice_image - owner: imgteam -- name: squidpy - owner: goeckslab -- name: vitessce_spatial - owner: goeckslab diff --git a/communities/microgalaxy/subdomain/tool_panel/spatial.yml.lock b/communities/microgalaxy/subdomain/tool_panel/spatial.yml.lock deleted file mode 100644 index 415c67d3..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/spatial.yml.lock +++ /dev/null @@ -1,41 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tool_panel_section_label: Spatial -tools: -- name: quantification - owner: perssond - revisions: - - 3a916c4e9f5f - tool_panel_section_id: spatial - tool_panel_section_label: Spatial -- name: cell_intensity_processing - owner: goeckslab - revisions: - - 5d541df02496 - tool_panel_section_id: spatial - tool_panel_section_label: Spatial -- name: s3segmenter - owner: perssond - revisions: - - 96d0d969ebc9 - tool_panel_section_id: spatial - tool_panel_section_label: Spatial -- name: slice_image - owner: imgteam - revisions: - - a72590196440 - tool_panel_section_id: spatial - tool_panel_section_label: Spatial -- name: squidpy - owner: goeckslab - revisions: - - d30ef0613122 - tool_panel_section_id: spatial - tool_panel_section_label: Spatial -- name: vitessce_spatial - owner: goeckslab - revisions: - - 7cc457aa78b1 - tool_panel_section_id: spatial - tool_panel_section_label: Spatial diff --git a/communities/microgalaxy/subdomain/tool_panel/tool_panel_view.yml b/communities/microgalaxy/subdomain/tool_panel/tool_panel_view.yml deleted file mode 100644 index 992f462b..00000000 --- a/communities/microgalaxy/subdomain/tool_panel/tool_panel_view.yml +++ /dev/null @@ -1,438 +0,0 @@ -name: Single Cell -type: generic -id: singlecell -items: -- id: general_section - text: General Tools - type: label -- sections: - # These will be named differently on each server: - - getext # "Get Data" - - send # "Send Data" - - collection_operations - - plots - - textutil - - filter - - group -- id: sc_tools - 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owner: ebi-gxa - revisions: - - 0db997e4a81d - tool_panel_section_label: Single-Cell -- name: seurat_scale_data - owner: ebi-gxa - revisions: - - 5e9ba303f9e1 - tool_panel_section_label: Single-Cell diff --git a/communities/microgalaxy/subdomain/usegalaxy.eu.yml b/communities/microgalaxy/subdomain/usegalaxy.eu.yml deleted file mode 100644 index 67143644..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.eu.yml +++ /dev/null @@ -1,55 +0,0 @@ -# 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 - -# ----------------------------------------------------------------------------- -# 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: Europe -nationality: European - -# Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.eu -subdomain: singlecell -root_domain: usegalaxy.eu - -# This will enable a feedback form on the webpage: -# feedback_email: help@mygalaxy.org - -quota_request_url: https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform -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: Galaxy Training Community chat - url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im - - title: Usegalaxy.eu chat - url: https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im - - title: Usegalaxy.org chat - url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im - -conclusion_extra_md: > -
- {% markdown_from_url 'https://raw.githubusercontent.com/galaxyproject/galaxy-hub/master/content/eu/common/data-policy.md' %} -
-
- -
- -# ----------------------------------------------------------------------------- -# Custom content relative to this file URL - -custom_css: usegalaxy.eu/static/custom.css -footer_md: usegalaxy.eu/templates/footer.html diff --git a/communities/microgalaxy/subdomain/usegalaxy.eu/static/custom.css b/communities/microgalaxy/subdomain/usegalaxy.eu/static/custom.css deleted file mode 100644 index a579d07b..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.eu/static/custom.css +++ /dev/null @@ -1,10 +0,0 @@ -#conclusionExtra h1 { - font-size: 1.5rem; - margin-bottom: 1rem; -} -#conclusionExtra { - font-size: 90%; -} -#conclusionExtra td { - font-size: 90%; -} \ No newline at end of file diff --git a/communities/microgalaxy/subdomain/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/subdomain/usegalaxy.eu/templates/footer.html deleted file mode 100644 index 0ff9c101..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.eu/templates/footer.html +++ /dev/null @@ -1,70 +0,0 @@ - diff --git a/communities/microgalaxy/subdomain/usegalaxy.org.au.yml b/communities/microgalaxy/subdomain/usegalaxy.org.au.yml deleted file mode 100644 index 0a032cc7..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.org.au.yml +++ /dev/null @@ -1,43 +0,0 @@ -# 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 - -# ----------------------------------------------------------------------------- -# Use these variables in MD/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: Australia -nationality: Australian - -# Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org.au -subdomain: singlecell -root_domain: usegalaxy.org.au - -# This will enable a feedback form on the webpage: -feedback_email: help@genome.edu.au - -# More variables for MD/HTML templating -support_url: https://site.usegalaxy.org.au/request -quota_request_url: https://site.usegalaxy.org.au/request/quota -data_policy_url: https://site.usegalaxy.org.au/about#data-privacy -terms_url: https://site.usegalaxy.org.au/about#terms-of-service - -help_links: - - title: Galaxy Australia Support - 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: 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 diff --git a/communities/microgalaxy/subdomain/usegalaxy.org.au/templates/footer.html b/communities/microgalaxy/subdomain/usegalaxy.org.au/templates/footer.html deleted file mode 100644 index fa4d580e..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.org.au/templates/footer.html +++ /dev/null @@ -1,119 +0,0 @@ - diff --git a/communities/microgalaxy/subdomain/usegalaxy.org.yml b/communities/microgalaxy/subdomain/usegalaxy.org.yml deleted file mode 100644 index 63934752..00000000 --- a/communities/microgalaxy/subdomain/usegalaxy.org.yml +++ /dev/null @@ -1,35 +0,0 @@ -# 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 - -# ----------------------------------------------------------------------------- -# 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: "" # ? -nationality: "" - -# Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell -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: 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 diff --git a/sources/bin/format_tools.sh b/sources/bin/format_tools.sh index 04c88095..ecf25c2a 100755 --- a/sources/bin/format_tools.sh +++ b/sources/bin/format_tools.sh @@ -1,13 +1,27 @@ #!/usr/bin/env bash -python sources/bin/create_interactive_table.py \ - --input "communities/all/resources/tools.tsv" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/all/resources/tools.html" +if [[ ! -z $1 && $1 == "test" ]]; then + python sources/bin/create_interactive_table.py \ + --input "communities/all/resources/test_tools.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/all/resources/tools.html" -python sources/bin/create_wordcloud.py \ - --input "communities/all/resources/tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ - --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ - --output "communities/all/resources/tools_wordcloud.png" \ \ No newline at end of file + python sources/bin/create_wordcloud.py \ + --input "communities/all/resources/test_tools.tsv" \ + --name-col "Galaxy wrapper id" \ + --stat-col "No. of tool users (5 years) - all main servers" \ + --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ + --output "communities/all/resources/tools_wordcloud.png" +else + python sources/bin/create_interactive_table.py \ + --input "communities/all/resources/tools.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/all/resources/tools.html" + + python sources/bin/create_wordcloud.py \ + --input "communities/all/resources/tools.tsv" \ + --name-col "Galaxy wrapper id" \ + --stat-col "No. of tool users (5 years) - all main servers" \ + --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ + --output "communities/all/resources/tools_wordcloud.png" +fi; \ No newline at end of file