Merge branch 'master' into create-pull-request/patch-1718247954

.github/workflows/main.yml

@@ -42,12 +42,14 @@ jobs:
         with:
           start: yarn serve
           wait-on: "http://localhost:8080"
-      - uses: actions/upload-artifact@v2
+      - name: Upload Cypress Screenshots
+        uses: actions/upload-artifact@v4
         with:
           name: cypress-screenshots
           path: cypress/screenshots
           if-no-files-found: ignore
-      - uses: actions/upload-artifact@v2
+      - name: Upload Cypress Videos
+        uses: actions/upload-artifact@v4
         with:
           name: cypress-videos
           path: cypress/videos

.github/workflows/optimize-images.yml

@@ -26,14 +26,17 @@ jobs:
   build:
     name: calibreapp/image-actions
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     # Only run on main repo on and PRs that match the main repo.
     if: |
       github.repository == 'galaxyproject/galaxy-hub' &&
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
       - name: Checkout Branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Compress Images
         id: calibre
         uses: calibreapp/image-actions@main
@@ -48,7 +51,7 @@ jobs:
         if: |
           github.event_name != 'pull_request' &&
           steps.calibre.outputs.markdown != ''
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v7
         with:
           title: Auto Compress Images
           branch-suffix: timestamp

content/admin/get-galaxy/index.md

@@ -19,15 +19,15 @@ If setting up or running a production Galaxy service or creating your own person
 If you do not have a Galaxy repository yet or you do not want to update the existing instance, run:
 
 ```
-$ git clone -b release_24.0 https://github.com/galaxyproject/galaxy.git
+$ git clone -b release_24.1 https://github.com/galaxyproject/galaxy.git
 ```
 
 ### Updating existing
 
 If you have an existing Galaxy repository and want to update it, run:
 
 ```
-$ git fetch origin && git checkout release_24.0 && git pull --ff-only origin release_24.0
+$ git fetch origin && git checkout release_24.1 && git pull --ff-only origin release_24.1
 ```
 
 

content/bare/eu/usegalaxy/main/index.md

@@ -4,9 +4,8 @@ title: Galaxy Europe
 
 <slot name="/bare/eu/usegalaxy/notices" />
 
-<Carousel />
+<!--Carousel /-->
 
-<br/>
 <br/>
 
 "Anyone, anywhere in the world should have free, unhindered access to not just my research, but to the research of every great and enquiring mind across the spectrum of human understanding." – Prof. Stephen Hawking

content/belgium/navbar.yml

@@ -51,5 +51,7 @@ right:
     target: "/projects/mpxv/"
   - label: VGP
     target: "/projects/vgp/"
+  - label: BRC Analytics
+    target: "https://brc-analytics.org/"
 - label: "@jxtx"
   target: https://jxtxfoundation.org/

content/blog/2024-06-14-CoC-EoY-2023/index.md

@@ -0,0 +1,42 @@
+---
+title: "Code Of Conduct Committee Annual Update "
+authors: "Ross Lazarus, Helena Rasche, Frederik Coppens, Michelle Savage"
+source_blog: ""
+date: "2024-06-14"
+---
+
+## Incident Report
+Incidents reported at GCC (June 2023): 0 <br />
+
+Incidents reported at EGD (June 2023): 0 <br />
+
+
+Lack of incidents being reported does not necessarily mean lack of incidents. 
+Please feel free to get in touch with the CoC Committee if you think that there have been incidents that have not yet been raised.
+
+
+## Changes to Code Of Conduct committee
+Change in membership - Assunta DeSanto has left the committee.
+
+## Procedures for changes to Code of Conduct
+CoC Committee members are now listed as codeowners of the file, ensuring that we are aware of any requested changes, and preventing 
+committee members from changing things without review. Review and update window will be held annually starting at GCC each year at a Bird of a Feather event (co-responding async document will be available for members who are not attending GCC in person).  The proposed changes will be shared in the Hub and we will solicit feedback for up to two months. Afterwards, the CoC will vote on the proposed changes and inputs, and ask the Exec Board to ratify our changes. Following the changes, we will publish the updates to the CoC, any incidents that took place and their outcome, and the minutes from Code of Conduct meetings.
+
+
+## Code Of Conduct Committee Meeting Minutes Summary 2022-2023
+
+### 11 April 2024
+
+#### Participants 
+Michelle, Ross, Asunta, Helena, Frederik
+
+### 1 June 2023
+
+#### Participants 
+Michelle, Ross, Helena, Frederik
+
+#### 11 October 2023
+
+#### Participants 
+Assunta, Bea, Ross, Helena, Frederik
+

content/blog/2024-07-29-galaxy-aquainfra/index.md

@@ -0,0 +1,11 @@
+---
+date: '2024-07-29'
+title: "The AquaINFRA Virtual Research Environment "
+tease: "Design rationale for using the Galaxy platform"
+authors: "Markus Konkol"
+external_url: "https://blog.52north.org/2024/07/25/the-aquainfra-virtual-research-environment-design-rationale-for-using-the-galaxy-platform/"
+source_blog_url: "https://blog.52north.org/" 
+source_blog: "52°North Blog"
+tags: [esg-wp5, esg, aquainfra, eosc]
+subsites: [all-eu, global]
+---

content/blog/2024-09-17-Reflections on GCC2024

@@ -0,0 +1 @@
+

content/blog/2024-11-elixir-exchange/index.md

@@ -0,0 +1,59 @@
+---
+title: "How I Learned to Wrap Tools from the Galaxy EU Team"
+date: "2024-11-05"
+authors: "Marisa Loach"
+tease: "An ELIXIR Staff Exchange to expand the single cell tools on Galaxy"
+---
+I am currently a PhD student at The Open University in the UK, where I reanalyse public single cell RNA sequencing data using Galaxy to explore how cells change in disease. However, I recently took a break from my project to learn how to add more tools to the Galaxy platform. As [my poster at GCC2024](https://f1000research.com/posters/13-806) explained, I went from being a user who wished for more tools to being a user-developer who can wrap those tools for herself.
+
+<p align="center">
+  <img src="./rocket-marisa.png" alt="A rocket with the Use Galaxy logo carries three users, one with a thought bubble reading I wish Galaxy had this tool... and the others with speech bubbles saying We need more tools for integration and annotation and Where is the latest version of Seurat. Two developers look on from behind their computer screens at a desk with the Galaxy Europe logo on it." width="400"/>
+</p>
+
+I was able to do this thanks to the **ELIXIR Staff Exchange Programme**, which enabled me to spend six months working with the Galaxy EU team in Freiburg. The project was initiated by my supervisor at The Open University, Wendi Bacon, who encouraged me to become part of the ELIXIR Single Cell Community, and Björn Grüning, who welcomed me into his team in Germany. The exchange gave me a chance to see the parts of Galaxy that users don’t usually encounter. It was amazing to see how hard the team works to keep Galaxy running and I was particularly impressed by how attentive they were to the Galaxy help forums and Matrix channels.
+
+## Wrapping Seurat for Galaxy
+
+During the exchange I learned how tools are incorporated into Galaxy through wrappers, which set out the tool requirements, the options that users will see on the interface, and the commands that Galaxy will perform when someone hits the Run Tool button. I used what I learned to wrap the latest version of the Seurat pipeline, which I was already familiar with thanks to my focus on single cell omics during my PhD.
+
+I drew on my experience of using Galaxy to reorganise the Seurat tools, grouping them together by theme, so that we now have wrappers for preprocessing, dimensional reduction, data integration, and other activities. Each of these wrappers contains a selection of related functions, including some that weren’t previously available on Galaxy. Once the tools were working, I also wrote a tutorial for the Galaxy Training Network (GTN) to help people start using them for their own analyses.
+
+### The New Seurat Toolsuite
+
+Load transcriptomic or CITEseq data into a Seurat Object, add QC metrics, and filter the dataset with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_create"><button type="button" class="btn btn-primary btn-lg">Seurat Create</button></a>
+</div><br>
+Prepare data for analysis with separate normalization, scaling, and feature selection functions or using SCTransform with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_preprocessing"><button type="button" class="btn btn-primary btn-lg">Seurat Preprocessing</button></a>
+</div><br>
+Calculate PCA, tSNE, or UMAP with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_reduce_dimension"><button type="button" class="btn btn-primary btn-lg">Seurat Run Dimensional Reduction</button></a>
+</div><br>
+Compute a neighborhood graph, apply clustering algorithms, and perform differential expression analysis with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_clustering"><button type="button" class="btn btn-primary btn-lg">Seurat Find Clusters</button></a>
+</div><br>
+Create plots such as violin plots, heatmaps, or dimensional reduction plots with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_plot"><button type="button" class="btn btn-primary btn-lg">Seurat Visualize</button></a>
+</div><br>
+Inspect or manipulate a Seurat Object (e.g. add more metadata, rename idents, subset data) with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_data"><button type="button" class="btn btn-primary btn-lg">Seurat Data Management</button></a>
+</div><br>
+Split, join, or integrate layers of data with:
+<div align="left">
+<a href="https://usegalaxy.eu/?tool_id=seurat_integrate"><button type="button" class="btn btn-primary btn-lg">Seurat Integrate</button></a>
+</div><br>
+
+## What I Learned About Galaxy
+
+The whole process gave me a deeper understanding of the tools as I had to decide which functions and parameters we should include and how they should be presented on the Galaxy interface. Every parameter had to be assigned the appropriate type and labelled with a helpful description. Seeing how the original tools turned into their Galaxy versions also gave me a new appreciation for how much easier my life is because I can use Galaxy for my PhD - it does a lot of the hard work for me!
+
+I really enjoyed tool wrapping as it allowed me to spend my days solving puzzles. Although it took a lot of work to wrap the entire Seurat pipeline, it was very rewarding to see the tools I wrapped appear on Galaxy and to know that people like me would soon be using them. I would definitely recommend anyone who is curious about tool wrapping to give it a go, especially if there's a tool that you wish was available on Galaxy. The GTN has some [tutorials](https://training.galaxyproject.org/training-material/topics/dev/) that can help you to get started and I'm sure that any Galaxy community would be just as happy as the [Single cell and SPatial Omics Community (SPOC)](https://galaxyproject.org/community/sig/singlecell/) to welcome new contributors.
+
+Thanks to the **ELIXIR Staff Exchange Programme** for funding the project, Pavan Videm for getting me started with tool wrapping, and my hosts at the University of Freiburg for helping me to make the most of my time in Germany!
+

content/careers/2020-11-hopkins-biostat/index.md

@@ -1,7 +1,7 @@
 ---
 title: "Research Associate in Biomedical Data Science"
 date: '2020-11-24'
-closes: 
+closes: '2021-11-24'
 summary: "Data science research and education focusing on genomics ([AnVIL](https://anvilproject.org/), [Genomic Data Science Community Network](http://www.gdscn.org/)), cancer ([ITCR](https://itcr.cancer.gov/))  or pain [A2CPS](https://a2cps.org/)."
 continent: NA
 location:

content/careers/2024-08-01-CMOOR/index.md

@@ -0,0 +1,11 @@
+---
+title: "Genomics Education Lead - Assistant Research Scientist"
+date: "2024-08-01"
+summary: "Join the [C-MOOR project](https://www.c-moor.org) and help transform genomics education by providing early research experiences for the next generation of data scientists. Our team is focused on integrating genomic data science into the curriculum, ensuring students gain hands-on research experience regardless of their institutional affiliation. As the Genomics Education Lead, you will create lessons, support instructors, and assess the impact of CUREs covering areas such as soil metagenomics and transcriptomics that will be used at JHU and our partners at 2- and 4-year institutions. This position is at the Assistant Research Scientist level and funded for two years, with additional employment contingent upon securing further funding."
+continent: NA
+location:
+  name: "Johns Hopkins University: Zanvyl Krieger School of Arts and Sciences: Department of Biology; Baltimore, MD, USA"
+location_url: "https://bio.jhu.edu/"
+external_url: "https://apply.interfolio.com/150737"
+contact: "Frederick Tan: [email protected]"
+---