From 5d57f42fd28e7eb8a9f76062cbca0a2a2e70e001 Mon Sep 17 00:00:00 2001 From: "galaxy-social-bot[bot]" <171031730+galaxy-social-bot[bot]@users.noreply.github.com> Date: Wed, 31 Jul 2024 00:24:25 +0000 Subject: [PATCH 1/4] Add Shiny phyloseq interactive tool available on usegalaxy.eu - practical outcome of the Bioconductor Hackathon --- .../2024-07-26-shiny-phyloseq-on-eu.md | 122 ++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md diff --git a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md new file mode 100644 index 0000000..e2e317b --- /dev/null +++ b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md @@ -0,0 +1,122 @@ +--- +media: +- mastodon-eu-freiburg +- matrix-eu-announce +- bluesky-galaxyproject +- linkedin-galaxyproject +mentions: + mastodon-eu-freiburg: + - galaxyproject@mstdn.science + bluesky-galaxyproject: + - galaxyproject.bsky.social + matrix-eu-announce: + - bgruening:matrix.org +hashtags: + mastodon-eu-freiburg: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - usegalaxy + - EOSC + - EuroScienceGateway + bluesky-galaxyproject: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - usegalaxy + - EOSC + - EuroScienceGateway + linkedin-galaxyproject: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - usegalaxy + - EOSC + - EuroScienceGateway +--- +📝 New blog post Released! + +Shiny phyloseq interactive tool (IT) +==================================== + + +[Shiny apps](https://shiny.posit.co/) are web apps using R functionality, that give easy responsive access to R packages. +Interactive tools are a great way to work with data interactively and responsive using Galaxy. In theory all shiny apps could become ITs, but so far the +wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the integration of Shiny apps as ITs, the Freiburg Galaxy team conducted a two\-day hackathon in February, collaborating with members from the Bioconductor community, including Charlotte Soneson, Hans\-Rudolf Hotz, and Federico Marini. During the event, best practices for developing ITs using Shiny apps were established, with a primary focus on creating a Docker image that can serve as a starting point for adding any Shiny app. +As a proof\-of\-concept the [shiny\-phyloseq app](https://github.com/joey711/shiny-phyloseq) has been wrapped as IT. +A fork of this Docker image tailored for the shiny app is available here: https://github.com/paulzierep/docker\-phyloseq. +The image can be run locally to test the app and then must be deployed to [quay.io](https://quay.io) or any other Docker registry. +This app allows to perform dynamic analysis of +metabarcoding/amplicon data such as: + + +* filter data based on metadata and taxonomy +* plot alpha diversity +* plot distance networks + + + +![Network](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Network.png) + + + +* ordination plots + + + +![Ordination](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Ordination.png) + + + +* heatmaps + + + +![Heatmap](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Heatmap.png) + + + +* trees + + + +![Tree](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Tree.png) + + + +* scatter plots +* bar charts + + + +![Barplot](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Barplot.png) + + + +The tools is available on usegalaxy.eu (https://usegalaxy.eu/?tool\_id\=interactive\_tool\_phyloseq\&version\=latest) and was integrated into a [dada2 based GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/tutorial.html) by BĂ©rĂ©nice Batut. + + +Data upload from Galaxy +----------------------- + + +Although the IT worked with the original shiny app. The shiny\-phyloseq app did not allow to upload amplicon data using command line arguments, which makes it difficult to allow for data input from Galaxy directly (downloading data from the Galaxy History and uploading to the IT via the web frontend would work though). Therefore, the tool was forked and modified to allow for additional data input. This functional adaptation of shiny\-apps to allow for non\-web based data upload is the only requirement to make any shiny app compatible with Galaxy based data upload. + + +The changes made to the original app can be found in this [git diff](https://github.com/joey711/shiny-phyloseq/compare/master...paulzierep:shiny-phyloseq:master). + + +Demo of the IT +-------------- + + +![Demo](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/alpha-div.gif) + + +Outlook +------- + + +To improve the usability and Galaxy\-interaction of the phyloseq\-shiny app we are working on the possibility to export data (figures, modified phyloseq objects) to the Galaxy history, either by collecting the data as outputs of the IT or by using utility functions such as put / get, that are used in other ITs like [RStudio](https://usegalaxy.eu/?tool_id=interactive_tool_rstudio&version=latest). + +https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ \ No newline at end of file From 96a3f6e6ea630dbb30c3a6171f900bdc4c5b0209 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 31 Jul 2024 09:40:13 +0200 Subject: [PATCH 2/4] Update 2024-07-26-shiny-phyloseq-on-eu.md --- .../2024-07-26-shiny-phyloseq-on-eu.md | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md index e2e317b..453e952 100644 --- a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md +++ b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md @@ -41,25 +41,30 @@ Shiny phyloseq interactive tool (IT) [Shiny apps](https://shiny.posit.co/) are web apps using R functionality, that give easy responsive access to R packages. -Interactive tools are a great way to work with data interactively and responsive using Galaxy. In theory all shiny apps could become ITs, but so far the -wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the integration of Shiny apps as ITs, the Freiburg Galaxy team conducted a two\-day hackathon in February, collaborating with members from the Bioconductor community, including Charlotte Soneson, Hans\-Rudolf Hotz, and Federico Marini. During the event, best practices for developing ITs using Shiny apps were established, with a primary focus on creating a Docker image that can serve as a starting point for adding any Shiny app. -As a proof\-of\-concept the [shiny\-phyloseq app](https://github.com/joey711/shiny-phyloseq) has been wrapped as IT. -A fork of this Docker image tailored for the shiny app is available here: https://github.com/paulzierep/docker\-phyloseq. +Interactive tools are a great way to work with data interactively and responsive using Galaxy. + + +In theory all shiny apps could become ITs, but so far the wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the integration of Shiny apps as ITs, the Freiburg Galaxy team conducted a two-day hackathon in February, collaborating with members from the Bioconductor community, including Charlotte Soneson, Hans-Rudolf Hotz, and Federico Marini. + + +During the event, best practices for developing ITs using Shiny apps were established, with a primary focus on creating a Docker image that can serve as a starting point for adding any Shiny app. +As a proof-of-concept the [shiny-phyloseq app](https://github.com/joey711/shiny-phyloseq) has been wrapped as IT. + + +A fork of this Docker image tailored for the shiny app is available here: https://github.com/paulzierep/docker-phyloseq. The image can be run locally to test the app and then must be deployed to [quay.io](https://quay.io) or any other Docker registry. + + This app allows to perform dynamic analysis of metabarcoding/amplicon data such as: - * filter data based on metadata and taxonomy * plot alpha diversity * plot distance networks - - ![Network](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Network.png) - * ordination plots @@ -119,4 +124,4 @@ Outlook To improve the usability and Galaxy\-interaction of the phyloseq\-shiny app we are working on the possibility to export data (figures, modified phyloseq objects) to the Galaxy history, either by collecting the data as outputs of the IT or by using utility functions such as put / get, that are used in other ITs like [RStudio](https://usegalaxy.eu/?tool_id=interactive_tool_rstudio&version=latest). -https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ \ No newline at end of file +https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ From 080e28ddfba220df12d4f97866986441da7b23ae Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Wed, 31 Jul 2024 10:49:32 +0200 Subject: [PATCH 3/4] Update 2024-07-26-shiny-phyloseq-on-eu.md --- .../2024-07-26-shiny-phyloseq-on-eu.md | 47 ++++--------------- 1 file changed, 10 insertions(+), 37 deletions(-) diff --git a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md index 453e952..4d4ee09 100644 --- a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md +++ b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md @@ -16,32 +16,31 @@ hashtags: - UseGalaxy - GalaxyProject - UniFreiburg - - usegalaxy - EOSC - EuroScienceGateway bluesky-galaxyproject: - UseGalaxy - GalaxyProject - UniFreiburg - - usegalaxy - EOSC - EuroScienceGateway linkedin-galaxyproject: - UseGalaxy - GalaxyProject - UniFreiburg - - usegalaxy - EOSC - EuroScienceGateway --- 📝 New blog post Released! +https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ + Shiny phyloseq interactive tool (IT) ==================================== - +![Demo of the new shiny phyloseq interactive tool running on Galaxy Europe](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/alpha-div.gif) [Shiny apps](https://shiny.posit.co/) are web apps using R functionality, that give easy responsive access to R packages. -Interactive tools are a great way to work with data interactively and responsive using Galaxy. +Interactive tools are a great way to work with data interactively and responsive using Galaxy. In theory all shiny apps could become ITs, but so far the wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the integration of Shiny apps as ITs, the Freiburg Galaxy team conducted a two-day hackathon in February, collaborating with members from the Bioconductor community, including Charlotte Soneson, Hans-Rudolf Hotz, and Federico Marini. @@ -61,67 +60,41 @@ metabarcoding/amplicon data such as: * filter data based on metadata and taxonomy * plot alpha diversity * plot distance networks - ![Network](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Network.png) - * ordination plots - - - ![Ordination](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Ordination.png) - - * heatmaps - - - ![Heatmap](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Heatmap.png) - - * trees - - - ![Tree](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Tree.png) - - * scatter plots * bar charts - - - ![Barplot](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Barplot.png) - -The tools is available on usegalaxy.eu (https://usegalaxy.eu/?tool\_id\=interactive\_tool\_phyloseq\&version\=latest) and was integrated into a [dada2 based GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/tutorial.html) by BĂ©rĂ©nice Batut. +The tool is available on usegalaxy.eu (https://usegalaxy.eu/?tool\_id\=interactive\_tool\_phyloseq\&version\=latest) and was integrated into a [dada2 based GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/tutorial.html) by BĂ©rĂ©nice Batut. Data upload from Galaxy ----------------------- +The IT worked with the original shiny\-phyloseq app, but the app did not allow to upload amplicon data via CLI arguments making data input from Galaxy incovenient (requiring users to download data from their Galaxy History, then upload it to the IT via the web frontend). -Although the IT worked with the original shiny app. The shiny\-phyloseq app did not allow to upload amplicon data using command line arguments, which makes it difficult to allow for data input from Galaxy directly (downloading data from the Galaxy History and uploading to the IT via the web frontend would work though). Therefore, the tool was forked and modified to allow for additional data input. This functional adaptation of shiny\-apps to allow for non\-web based data upload is the only requirement to make any shiny app compatible with Galaxy based data upload. - - -The changes made to the original app can be found in this [git diff](https://github.com/joey711/shiny-phyloseq/compare/master...paulzierep:shiny-phyloseq:master). +Therefore, the tool was forked and modified to allow for additional data input. This functional adaptation of shiny\-apps to allow for non\-web based data upload is the only requirement to make any shiny app compatible with Galaxy based data upload. -Demo of the IT --------------- - -![Demo](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/alpha-div.gif) +The changes made to the original app can be found in this [git diff](https://github.com/joey711/shiny-phyloseq/compare/master...paulzierep:shiny-phyloseq:master). Outlook ------- +To improve the usability and Galaxy\-interaction of the phyloseq\-shiny app we are working on the possibility to export data (figures, modified phyloseq objects) to the Galaxy history. -To improve the usability and Galaxy\-interaction of the phyloseq\-shiny app we are working on the possibility to export data (figures, modified phyloseq objects) to the Galaxy history, either by collecting the data as outputs of the IT or by using utility functions such as put / get, that are used in other ITs like [RStudio](https://usegalaxy.eu/?tool_id=interactive_tool_rstudio&version=latest). -https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ +This could be done either by collecting the data as outputs of the IT or by using utility functions such as put / get, that are used in other ITs like [RStudio](https://usegalaxy.eu/?tool_id=interactive_tool_rstudio&version=latest). From 9768b0deaccc89d3b272775591a0b976b34ec242 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Wed, 31 Jul 2024 11:02:17 +0200 Subject: [PATCH 4/4] Update 2024-07-26-shiny-phyloseq-on-eu.md --- .../galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md index 4d4ee09..ca561f8 100644 --- a/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md +++ b/posts/feed_bot/galaxy_europe/2024-07-26-shiny-phyloseq-on-eu.md @@ -37,17 +37,15 @@ https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ Shiny phyloseq interactive tool (IT) ==================================== - ![Demo of the new shiny phyloseq interactive tool running on Galaxy Europe](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/alpha-div.gif) [Shiny apps](https://shiny.posit.co/) are web apps using R functionality, that give easy responsive access to R packages. Interactive tools are a great way to work with data interactively and responsive using Galaxy. -In theory all shiny apps could become ITs, but so far the wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the integration of Shiny apps as ITs, the Freiburg Galaxy team conducted a two-day hackathon in February, collaborating with members from the Bioconductor community, including Charlotte Soneson, Hans-Rudolf Hotz, and Federico Marini. +In theory all shiny apps could become ITs, but so far wrapping and deployment of shiny apps as ITs was technically challenging. To facilitate the process, the Freiburg Galaxy team conducted a two-day hackathon in February, collaborating with members of the Bioconductor community, including Charlotte Soneson, Hans-Rudolf Hotz, and Federico Marini. -During the event, best practices for developing ITs using Shiny apps were established, with a primary focus on creating a Docker image that can serve as a starting point for adding any Shiny app. -As a proof-of-concept the [shiny-phyloseq app](https://github.com/joey711/shiny-phyloseq) has been wrapped as IT. +During the event, best practices for developing ITs using Shiny apps were established, with a focus on creating a Docker image that can serve as a starting point for adding any Shiny app and the [shiny-phyloseq app](https://github.com/joey711/shiny-phyloseq) as a proof-of-concept target. A fork of this Docker image tailored for the shiny app is available here: https://github.com/paulzierep/docker-phyloseq. @@ -61,16 +59,12 @@ metabarcoding/amplicon data such as: * plot alpha diversity * plot distance networks ![Network](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Network.png) - * ordination plots ![Ordination](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Ordination.png) - * heatmaps ![Heatmap](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Heatmap.png) - * trees ![Tree](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Tree.png) - * scatter plots * bar charts ![Barplot](https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/Barplot.png) @@ -82,7 +76,7 @@ The tool is available on usegalaxy.eu (https://usegalaxy.eu/?tool\_id\=interacti Data upload from Galaxy ----------------------- -The IT worked with the original shiny\-phyloseq app, but the app did not allow to upload amplicon data via CLI arguments making data input from Galaxy incovenient (requiring users to download data from their Galaxy History, then upload it to the IT via the web frontend). +The original shiny\-phyloseq app worked in an IT, but did not allow to upload amplicon data via CLI arguments making data input from Galaxy incovenient (requiring users to download data from their Galaxy History, then upload it to the IT via the web frontend). Therefore, the tool was forked and modified to allow for additional data input. This functional adaptation of shiny\-apps to allow for non\-web based data upload is the only requirement to make any shiny app compatible with Galaxy based data upload.