From d48d52ab27cdccca402697f284f1222b8f47feb1 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 22:49:17 +0100 Subject: [PATCH 01/23] close tag --- subdomains/singlecell/sections/1_beginner.yml | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index ed77a0bf..a436e51a 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -46,7 +46,7 @@ tabs: - 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 + EBI SCXA Data Retrieval button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa" button_icon: tool button_tip: Run tool @@ -64,15 +64,15 @@ tabs: - title_md: Importing 10X Files description_md: > You can find many tools for importing 10X formatted data into target datatypes. - Scanpy Read10x + Scanpy Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x" button_icon: tool button_tip: Run tool - Seurat Read10x + Seurat Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x" button_icon: tool button_tip: Run tool - DropletUtils Read10x + DropletUtils Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x" button_icon: tool button_tip: Run tool @@ -85,19 +85,19 @@ tabs: - title_md: Data conversion tools description_md: > There are a few key tools in Galaxy for interconverting and manipulating objects in Galaxy. This list is not exhaustive. - SCEasy Converter + SCEasy Converter This tool allows you to convert between *AnnData*, *Loom*, *Seurat*, and *Singlecellexperiment* formats. button_link: "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert" button_icon: tool button_tip: Run tool description_md: > - Manipulate AnnData + Manipulate AnnData Under **Function to manipulate the object** you'll find key manipulations 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 the metadata. button_link: "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate" button_icon: tool button_tip: Run tool description_md: > - AnnData Operations + AnnData Operations This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops" button_icon: tool @@ -115,9 +115,9 @@ tabs: heading_md: > There are a few key tools for visualising single-cell data in Galaxy. content: - - title_md: Plot with Scanpy + - title_md: Plot with Scanpy description_md: > - Plot with Scanpy + Plot with Scanpy This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. inputs: - anndata @@ -125,9 +125,9 @@ tabs: button_link: "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot" button_icon: tool button_tip: Run tool - - title_md: Scanpy PlotEmbed + - title_md: Scanpy PlotEmbed description_md: > - Scanpy PlotEmbed + Scanpy PlotEmbed This tool allows you to plot embeddings like UMAPs. inputs: - anndata @@ -135,9 +135,9 @@ tabs: button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed" button_icon: tool button_tip: Run tool - - title_md: Scanpy PlotTrajectory + - title_md: Scanpy PlotTrajectory description_md: > - Scanpy PlotTrajectory + Scanpy PlotTrajectory This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. inputs: - anndata @@ -145,9 +145,9 @@ tabs: button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory" button_icon: tool button_tip: Run tool - - title_md: Scanpy Plot dimension reduction + - title_md: Scanpy Plot dimension reduction description_md: > - Scanpy Plot dimension reduction + Scanpy Plot dimension reduction This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. inputs: - RDS with a Seurat Object @@ -158,9 +158,9 @@ tabs: button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot" button_icon: tool button_tip: Run tool - - title_md: Plot with Seurat + - title_md: Plot with Seurat description_md: > - Plot with Seurat + Plot with Seurat This tool allows you to plot gene expressions, such as with Violin Plots. inputs: - RDS with a Seurat Object From 39ce634b00a5d9f9941439e157604f93709c1c1a Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 22:52:19 +0100 Subject: [PATCH 02/23] fix icons --- subdomains/singlecell/sections/1_beginner.yml | 24 +++++++++---------- .../singlecell/sections/4_community.yml | 2 +- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index a436e51a..30ed9075 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -48,7 +48,7 @@ tabs: 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: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa" - button_icon: tool + button_icon: run button_tip: Run tool description_md: > You can learn more by following our dedicated to tutorial for importing files from public atlases. @@ -66,15 +66,15 @@ tabs: You can find many tools for importing 10X formatted data into target datatypes. Scanpy Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x" - button_icon: tool + button_icon: run button_tip: Run tool Seurat Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x" - button_icon: tool + button_icon: run button_tip: Run tool DropletUtils Read10x button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x" - button_icon: tool + button_icon: run button_tip: Run tool - id: data_convert @@ -88,19 +88,19 @@ tabs: SCEasy Converter This tool allows you to convert between *AnnData*, *Loom*, *Seurat*, and *Singlecellexperiment* formats. button_link: "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert" - button_icon: tool + button_icon: run button_tip: Run tool description_md: > Manipulate AnnData Under **Function to manipulate the object** you'll find key manipulations 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 the metadata. button_link: "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate" - button_icon: tool + button_icon: run button_tip: Run tool description_md: > AnnData Operations This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops" - button_icon: tool + button_icon: run button_tip: Run tool content: - title_md: Data conversion training @@ -123,7 +123,7 @@ tabs: - anndata - hdf5 button_link: "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot" - button_icon: tool + button_icon: run button_tip: Run tool - title_md: Scanpy PlotEmbed description_md: > @@ -133,7 +133,7 @@ tabs: - anndata - hdf5 button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed" - button_icon: tool + button_icon: run button_tip: Run tool - title_md: Scanpy PlotTrajectory description_md: > @@ -143,7 +143,7 @@ tabs: - anndata - hdf5 button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory" - button_icon: tool + button_icon: run button_tip: Run tool - title_md: Scanpy Plot dimension reduction description_md: > @@ -156,7 +156,7 @@ tabs: - Loom - AnnData button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot" - button_icon: tool + button_icon: run button_tip: Run tool - title_md: Plot with Seurat description_md: > @@ -169,7 +169,7 @@ tabs: - Loom - AnnData button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot" - button_icon: tool + button_icon: run button_tip: Run tool - id: help diff --git a/subdomains/singlecell/sections/4_community.yml b/subdomains/singlecell/sections/4_community.yml index 8f620509..08b3df6c 100644 --- a/subdomains/singlecell/sections/4_community.yml +++ b/subdomains/singlecell/sections/4_community.yml @@ -16,7 +16,7 @@ tabs: Check out our site and join our community! [Galaxy Single-cell & sPatial Omics **(SPOC)** Community of Practice])(https://galaxyproject.org/community/sig/singlecell/) button_link: "https://galaxyproject.org/community/sig/singlecell/" - button_icon: site + button_icon: run button_tip: Visit SPOC - title_md: Contributors description_md: > From 18a218ca52c5412941aa2c59874bf5e8f6fd92b3 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 22:53:51 +0100 Subject: [PATCH 03/23] add gap --- subdomains/singlecell/sections/1_beginner.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index 30ed9075..fda2d3a3 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -46,6 +46,7 @@ tabs: - 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: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa" button_icon: run From 6c5691b6907c75f5e64bf66e7c46c95f9b4fefd9 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 22:58:30 +0100 Subject: [PATCH 04/23] remove double-printing the tool names --- subdomains/singlecell/sections/1_beginner.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index fda2d3a3..c69d336d 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -118,7 +118,6 @@ tabs: content: - title_md: Plot with Scanpy description_md: > - Plot with Scanpy This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. inputs: - anndata @@ -128,7 +127,6 @@ tabs: button_tip: Run tool - title_md: Scanpy PlotEmbed description_md: > - Scanpy PlotEmbed This tool allows you to plot embeddings like UMAPs. inputs: - anndata @@ -138,7 +136,6 @@ tabs: button_tip: Run tool - title_md: Scanpy PlotTrajectory description_md: > - Scanpy PlotTrajectory This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. inputs: - anndata @@ -148,7 +145,6 @@ tabs: button_tip: Run tool - title_md: Scanpy Plot dimension reduction description_md: > - Scanpy Plot dimension reduction This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. inputs: - RDS with a Seurat Object @@ -161,7 +157,6 @@ tabs: button_tip: Run tool - title_md: Plot with Seurat description_md: > - Plot with Seurat This tool allows you to plot gene expressions, such as with Violin Plots. inputs: - RDS with a Seurat Object From 0b9651ac260dbbde739b8f75c667876405e6ce76 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 22:59:48 +0100 Subject: [PATCH 05/23] fix iframe height --- subdomains/singlecell/sections/1_beginner.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index c69d336d..f7b9b10c 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -181,7 +181,7 @@ tabs: description_md: > - title_md: Is there a help forum? description_md: > From 294b1dae9ddd61946b22e73982f05299bf2bf97b Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:01:44 +0100 Subject: [PATCH 06/23] turn tags into a list --- subdomains/singlecell/sections/3_advanced.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index abba6888..b412dcd8 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -6,11 +6,11 @@ tabs: heading_md: > Workflows are chains of of tools that can be run together at the click of a button. The following tabs contain both peer reviewed and community submitted workflows. Common workflow tags for our community are: - - single-cell - - training (for workflows that correspond to the Galaxy Training Network's tutorials) - - data interoperability - - deconvolution - - spatial omics + -
  • single-cell
    • + -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • + -
  • data interoperability
    • + -
  • deconvolution
    • + -
  • spatial omics

    • Tag your workflows with #single-cell and share publicly with other users! From fc17ef904cc8fb27167fa4154c6b96d90cf4dcca Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:04:12 +0100 Subject: [PATCH 07/23] fix workflowhub link --- subdomains/singlecell/sections/3_advanced.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index b412dcd8..f767759d 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -4,7 +4,8 @@ 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 following tabs contain both peer reviewed and community submitted workflows. + Workflows are chains of of tools that can be run together at the click of a button. +

    The following tabs contain both peer reviewed and community submitted workflows.

    Common workflow tags for our community are: -
  • single-cell
    • -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • @@ -27,7 +28,7 @@ tabs: - id: workflows2 title: Peer-reviewed workflows heading_md: > - You can see workflows before that have been reviewed by scientists. + You can browse through workflows before that have been reviewed by scientists. content: - title_md: IWC description_md: > @@ -36,7 +37,7 @@ tabs: - title_md: WorkflowHub description_md: > WorkflowHub hosts high quality workflows. You can explore single-cell Galaxy workflows from WorkflowHub below. - + - id: workflows3 title: Community workflows From 6a321e583db4d4cde37d4ef9b3274796919672af Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:08:01 +0100 Subject: [PATCH 08/23] add workflow sharing --- subdomains/singlecell/sections/3_advanced.yml | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index f767759d..700f647e 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -46,13 +46,12 @@ tabs: content: - title_md: Community Workflows 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! - - It's even possible to do an - {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html) - to find exactly what you need. + Search through community workflows tagged with #single-cell. + - title_md: Bespoke workflow search description_md: > @@ -66,10 +65,8 @@ tabs: - title_md: How to share your workflow 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! - - It's even possible to do an - {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html) - to find exactly what you need. + From 40d2acbf1ba8c2de2e2940b40f6c22cf1e3c716a Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:09:46 +0100 Subject: [PATCH 09/23] add contributors --- subdomains/singlecell/sections/4_community.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/subdomains/singlecell/sections/4_community.yml b/subdomains/singlecell/sections/4_community.yml index 08b3df6c..484d3c93 100644 --- a/subdomains/singlecell/sections/4_community.yml +++ b/subdomains/singlecell/sections/4_community.yml @@ -8,7 +8,7 @@ tabs: description_md: > - title_md: Join our community! description_md: > @@ -22,18 +22,20 @@ tabs: description_md: > ### Contributors - - also Gareth & Cameron! + - [Wendi Bacon](https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/) + + - [Cameron Hyde](https://github.com/neoformit) - [Mehmet Tekman](https://github.com/mtekman) - [Pavankumar Videm](https://github.com/pavanvidem) - - [Wendi Bacon](https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/) - - [Pablo Moreno](https://github.com/pcm32) - [José Domínguez](https://github.com/kysrpex) + - [Gareth Price](https://github.com/GarethPrice-Aus) + - [Alex Ostrovsky](https://github.com/astrovsky01) - [Andrey Solovyev](https://github.com/a-solovyev12) From 4f9e478f54782f9966a5bab3d88212d36642dac1 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:13:04 +0100 Subject: [PATCH 10/23] add line separations --- subdomains/singlecell/sections/4_community.yml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/subdomains/singlecell/sections/4_community.yml b/subdomains/singlecell/sections/4_community.yml index 484d3c93..98a4dee4 100644 --- a/subdomains/singlecell/sections/4_community.yml +++ b/subdomains/singlecell/sections/4_community.yml @@ -8,13 +8,15 @@ tabs: description_md: > - title_md: Join our community! description_md: > - This Galaxy space is the result of seemingly infinite hours of hard work by a number of people. 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! - [Galaxy Single-cell & sPatial Omics **(SPOC)** Community of Practice])(https://galaxyproject.org/community/sig/singlecell/) +

    This Galaxy space is the result of seemingly infinite hours of hard work by a number of people.

    +

    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!

    +

    [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/)

    button_link: "https://galaxyproject.org/community/sig/singlecell/" button_icon: run button_tip: Visit SPOC @@ -83,7 +85,7 @@ tabs: heading_md: > content: [] From 1287dc2a2dea21bced07ae584d2cc8c928bd0372 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:17:28 +0100 Subject: [PATCH 11/23] explain links --- subdomains/singlecell/base.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subdomains/singlecell/base.yml b/subdomains/singlecell/base.yml index 272dd664..cb34d2c6 100644 --- a/subdomains/singlecell/base.yml +++ b/subdomains/singlecell/base.yml @@ -28,15 +28,15 @@ terms_url: https://usegalaxy.org/static/terms.html help_links: - title: General Galaxy support url: https://galaxyproject.org/support/ - - title: Single Cell community help forum - url: https://usegalaxy-eu.github.io/scrna + - 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 Forum + - title: Galaxy Training Network Slack workspace url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg - - title: Single cell Galaxy user community chat room - on Slack! + - title: Single cell Slack channel (#single-cell-users) url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7 - - title: Single cell Galaxy user community chat room + - 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 From 444fa18a0377e39ea7aaeabbcfde382ffd5b65c7 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:18:24 +0100 Subject: [PATCH 12/23] change iframe sizing --- subdomains/singlecell/sections/1_beginner.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index f7b9b10c..9ded2f39 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -175,13 +175,13 @@ tabs: description_md: > - title_md: How can I troubleshoot? description_md: > - title_md: Is there a help forum? description_md: > From be24fa5dfc73d32b55be9633a62ad5a8deca1a2b Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:19:00 +0100 Subject: [PATCH 13/23] fix list format --- subdomains/singlecell/sections/3_advanced.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index 700f647e..a7380e8d 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -7,11 +7,11 @@ tabs: Workflows are chains of of tools that can be run together at the click of a button.

    The following tabs contain both peer reviewed and community submitted workflows.

    Common workflow tags for our community are: - -
  • single-cell
    • - -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • - -
  • data interoperability
    • - -
  • deconvolution
    • - -
  • spatial omics
    • +
  • single-cell
    • +
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • +
  • data interoperability
    • +
  • deconvolution
    • +
  • spatial omics

    • Tag your workflows with #single-cell and share publicly with other users! From e1727e279294dbad26561870694d1997fd080944 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:19:24 +0100 Subject: [PATCH 14/23] move instructions --- subdomains/singlecell/sections/3_advanced.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index a7380e8d..fdaa0c29 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -5,6 +5,10 @@ tabs: title: Workflow Best Practices heading_md: > Workflows are chains of of tools that can be run together at the click of a button. +

    + Tag your workflows + with #single-cell and share publicly with other users! +

    The following tabs contain both peer reviewed and community submitted workflows.

    Common workflow tags for our community are:
  • single-cell
    • @@ -12,10 +16,7 @@ tabs:
  • data interoperability
  • deconvolution
  • spatial omics
    • -

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

    + content: - title_md: How to tag a workflow description_md: > From f2288fdac5e86687ab1047282555b776e3bc62a2 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:21:44 +0100 Subject: [PATCH 15/23] separate lines --- subdomains/singlecell/sections/3_advanced.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index fdaa0c29..3210d884 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -33,7 +33,7 @@ tabs: content: - title_md: IWC description_md: > - IWC is a label given to peer-reviewed workflows within Galaxy. + IWC is an **owner** of peer-reviewed, publicly shared workflows within Galaxy. - title_md: WorkflowHub description_md: > @@ -43,7 +43,8 @@ tabs: - 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. + 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: > From a225cafeaa3f3431aae240edfb0077918a2bc258 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:23:33 +0100 Subject: [PATCH 16/23] fix iframe --- subdomains/singlecell/sections/3_advanced.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index 3210d884..badb0025 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -61,14 +61,20 @@ tabs: {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_icon: run + button_tip: Launch site in tutorial-mode + It's even possible to do an {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html) to find exactly what you need. + button_icon: tutorial + button_tip: Launch tutorial + - title_md: How to share your workflow description_md: > From 7f70896e5823f52b11ccc1c45a22f5e9661c772a Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:25:27 +0100 Subject: [PATCH 17/23] update html to md text --- subdomains/singlecell/sections/4_community.yml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/subdomains/singlecell/sections/4_community.yml b/subdomains/singlecell/sections/4_community.yml index 98a4dee4..5fe69dfb 100644 --- a/subdomains/singlecell/sections/4_community.yml +++ b/subdomains/singlecell/sections/4_community.yml @@ -8,15 +8,18 @@ tabs: description_md: > - title_md: Join our community! description_md: > -

    This Galaxy space is the result of seemingly infinite hours of hard work by a number of people.

    -

    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!

    -

    [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/)

    + This Galaxy space is the result of seemingly infinite hours of hard work by a number of people. + + 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_icon: run button_tip: Visit SPOC From 69244acc8ebc00d1351e6b33d56dcb023dbd6502 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:28:34 +0100 Subject: [PATCH 18/23] rearrange help tabs --- subdomains/singlecell/sections/1_beginner.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index 9ded2f39..a95b9954 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -175,18 +175,18 @@ tabs: description_md: > + - title_md: Is there a help forum? + description_md: > + + [Single cell help forum](https://help.galaxyproject.org/tag/scrna) - title_md: How can I troubleshoot? description_md: > - - title_md: Is there a help forum? - description_md: > - - [Single cell help forum](https://help.galaxyproject.org/tag/scrna) - 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 From aa09e1a77383ef68057fcf5daf6ccc80e8d523fd Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:28:57 +0100 Subject: [PATCH 19/23] rearrange tabs --- subdomains/singlecell/sections/3_advanced.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index badb0025..760d12d6 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -9,13 +9,13 @@ tabs: Tag your workflows with #single-cell and share publicly with other users!

    -

    The following tabs contain both peer reviewed and community submitted workflows.

    Common workflow tags for our community are:
  • single-cell
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
  • data interoperability
  • deconvolution
  • spatial omics
    • +

    The following tabs contain both peer reviewed and community submitted workflows.

    content: - title_md: How to tag a workflow From ad8a0c6e0bdf54ce6b7de089b9b01ae897603b64 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:29:29 +0100 Subject: [PATCH 20/23] more iframe --- subdomains/singlecell/sections/3_advanced.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index 760d12d6..5f1ce3e3 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -75,6 +75,6 @@ tabs: description_md: > From 600171fb15a1916e8c75a3b9e74862b15b95ac56 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:31:32 +0100 Subject: [PATCH 21/23] fix lines --- subdomains/singlecell/sections/4_community.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/subdomains/singlecell/sections/4_community.yml b/subdomains/singlecell/sections/4_community.yml index 5fe69dfb..c6c57714 100644 --- a/subdomains/singlecell/sections/4_community.yml +++ b/subdomains/singlecell/sections/4_community.yml @@ -12,11 +12,12 @@ tabs: - title_md: Join our community! description_md: > - This Galaxy space is the result of seemingly infinite hours of hard work by a number of people. + + 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. + 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! From f6f6aeb339aaaf539d9555d1689c196faa1a000b Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:33:20 +0100 Subject: [PATCH 22/23] rearrange text --- subdomains/singlecell/sections/3_advanced.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/subdomains/singlecell/sections/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml index 5f1ce3e3..ac1bf9da 100644 --- a/subdomains/singlecell/sections/3_advanced.yml +++ b/subdomains/singlecell/sections/3_advanced.yml @@ -5,17 +5,16 @@ tabs: 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 #single-cell and share publicly with other users!

    - Common workflow tags for our community are: -
  • single-cell
    • + Additional common workflow tags for our community are:
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
  • data interoperability
  • deconvolution
  • spatial omics
    • -

    The following tabs contain both peer reviewed and community submitted workflows.

    content: - title_md: How to tag a workflow From 052a26d069e4a93273901b2926990d2613861cd8 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:37:02 +0100 Subject: [PATCH 23/23] centre the image --- subdomains/singlecell/templates/intro.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subdomains/singlecell/templates/intro.html b/subdomains/singlecell/templates/intro.html index 1628d098..cac4408b 100644 --- a/subdomains/singlecell/templates/intro.html +++ b/subdomains/singlecell/templates/intro.html @@ -7,7 +7,9 @@ Access Single Cell Omics analysis tutorials, tools, and workflows that let you analyse data without programming experience or private infrastructure.

    - Word cloud of common single cell tools including Seurat and Scanpy +
    + Word cloud of common single cell tools including Seurat and Scanpy +