Merge branch 'scottcain-tacc-pr' of https://github.com/galaxyproject/…

…galaxy-hub into scottcain-tacc-pr

.github/workflows/main.yml

@@ -2,53 +2,70 @@ name: PR Tests
 on: 
   pull_request:
   workflow_dispatch:
+
 concurrency:
   group: primary-tests-${{ github.head_ref }}
   cancel-in-progress: true
+
 env:
   NODE_OPTIONS: --max-old-space-size=4096
+
 jobs:
   build-and-test:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
+      - name: Checkout Repository
         uses: actions/checkout@v3
-      - name: Setup node
-        uses: actions/setup-node@v2
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
         with:
-          node-version: '16'
-      - name: Get yarn cache directory path
+          node-version: '18'
+
+      - name: Get Yarn Cache Directory Path
         id: yarn-cache-dir-path
-        run: echo "::set-output name=dir::$(yarn cache dir)"
-      - uses: actions/cache@v1
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
+
+      - name: Cache Yarn Dependencies
+        uses: actions/cache@v3
         id: yarn-cache
         with:
           path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
           key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
           restore-keys: |
             ${{ runner.os }}-yarn-
-      - name: Install project dependencies
-        run: yarn --prefer-offline
-      - name: Jest Tests
+
+      - name: Install Project Dependencies
+        run: yarn install --prefer-offline
+
+      - name: Run Jest Tests
         run: yarn jest
-      - name: Build static site
+
+      - name: Build Static Site
         run: yarn build
+
       - name: Serve and Check Links
-        # Looks weird, but this works significantly better than running it
-        # through a single node process
-        run: yarn run serve & (sleep 5 && yarn run links:internal)
-      - name: Cypress run
-        uses: cypress-io/github-action@v2
+        run: |
+          yarn serve &
+          sleep 5
+          yarn links:internal
+
+      - name: Run Cypress Tests
+        uses: cypress-io/github-action@v4
         with:
           start: yarn serve
           wait-on: "http://localhost:8080"
+
       - name: Upload Cypress Screenshots
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: cypress-screenshots
           path: cypress/screenshots
           if-no-files-found: ignore
+
       - name: Upload Cypress Videos
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: cypress-videos

.github/workflows/publish.yml

@@ -15,21 +15,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup node
-        uses: actions/setup-node@v2
+        uses: actions/setup-node@v4
         with:
           node-version: '16'
-      - name: Get yarn cache directory path
-        id: yarn-cache-dir-path
-        run: echo "::set-output name=dir::$(yarn cache dir)"
-      - uses: actions/cache@v1
-        id: yarn-cache
-        with:
-          path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
-          key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-yarn-
+          cache: 'yarn'
       - name: Install project dependencies
         run: yarn --prefer-offline
       - name: Build static site

content/admin/python/index.md

@@ -2,7 +2,7 @@
 title: Supported Python versions
 ---
 
-Galaxy's core functionality is currently supported on Python **3.7** or newer.
+Galaxy's core functionality is currently supported on Python **3.8** or newer.
 
 If Galaxy complains about the version of Python you are using:
 

content/community/sig/small-scale-admins/index.md

@@ -8,11 +8,11 @@ title: "Small scale Galaxy Admins Community of Practice"
 
 # Who are we?
 
-We are a group of admins who maintain a (small) (local) Galaxy server. Having grown out of the "Small Scale Servers" subcommittee of the [Global Galaxy Steering Committee](https://galaxyproject.org/community/steering/), our meetings are now taking place every two months. We discuss issues, problems, and of course solutions we encounter as maintainers of a non usegalaxy.* instance, which very often are very specific (and not covered by the Galaxy code base). We have different backgrounds and individual experiences. We do not have the same amount of time dedicated to administering our galaxy instance.
+We are a group of admins who maintain a (small) (local) Galaxy server. Having grown out of the "Small Scale Servers" subcommittee of the [Global Galaxy Steering Committee](https://galaxyproject.org/community/steering/), our meetings are now taking place every month. We discuss issues, problems, and of course solutions we encounter as maintainers of a non usegalaxy.* instance, which very often are very specific (and not covered by the Galaxy code base). We have different backgrounds and individual experiences. We do not have the same amount of time dedicated to administering our galaxy instance.
 We very much welcome new people who are just starting setting up a local Galaxy server or are only considering doing so.
 
 # How can you contact us or join us?
-We meet every 2 months by zoom. Check our next meeting in the [Galaxy WGs Google Calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com) and just join.
+We meet every month by zoom. Check our next meeting in the [Galaxy WGs Google Calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com) and just join.
 Occasionally, we organize a BoF at GCC or regional Galaxy meetings/workshops
 We have a [mailing list](https://lists.galaxyproject.org/lists/small-scale-admins.lists.galaxyproject.org/).
 We intentionally do not have chat but if you have a emergency admin question, please ask it to the [matrix channel](https://matrix.to/#/#galaxyproject_admins:gitter.im) 

content/events/2024-11-19-GalaxyBrazil/index.md

@@ -6,7 +6,7 @@ continent: SA
 location:
   name: "Curitiba, Brazil"
 gtn: false
-contact: "Anton Nekrutenk"
+contact: "Anton Nekrutenko"
 tags: [workshop, training]
 subsites: [all]
 ---

content/events/2024-12-small-scale/index.md

@@ -0,0 +1,25 @@
+---
+title: Small Scale Galaxy Admins Meeting
+date: '2024-12-19'
+days: 1
+continent: GL
+location:
+  name: Online, Global
+gtn: false
+contact:  Lucille Delisle, Hans-Rudolf Hotz
+tags:
+subsites: [all-eu, global, us]
+---
+
+
+
+Please <a href="https://epfl.zoom.us/j/69775900853?pwd=R1gzbllUZzg0RFUrM0Mzd2MvczE3Zz09">join us</a> 
+at 3 PM CET (<a href="https://www.timeanddate.com/worldclock/fixedtime.html?msg=Small+Scale+Galaxy+Admins+Meeting&iso=20241219T15&p1=945&ah=1">see in your timezone</a>) 
+for a discussion about general and current problems you encounter as a maintainer of a Galaxy server.
+
+
+
+---
+
+The [Small Scale Galaxy Admins group](https://galaxyproject.org/community/sig/small-scale-admins/) is a [Galaxy community of practice](https://galaxyproject.org/community/sig/#communities-of-practice).
+The meetings are taking place every month and are listed in the [Galaxy WG calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com).

content/events/2025-01-small-scale/index.md

@@ -0,0 +1,25 @@
+---
+title: Small Scale Galaxy Admins Meeting
+date: '2025-01-16'
+days: 1
+continent: GL
+location:
+  name: Online, Global
+gtn: false
+contact:  Lucille Delisle, Hans-Rudolf Hotz
+tags:
+subsites: [all-eu, global, us]
+---
+
+
+
+Please <a href="https://epfl.zoom.us/j/69775900853?pwd=R1gzbllUZzg0RFUrM0Mzd2MvczE3Zz09">join us</a> 
+at 3 PM CET (<a href="https://www.timeanddate.com/worldclock/fixedtime.html?msg=Small+Scale+Galaxy+Admins+Meeting&iso=20250116T15&p1=945&ah=1">see in your timezone</a>) 
+for a discussion about general and current problems you encounter as a maintainer of a Galaxy server.
+
+
+
+---
+
+The [Small Scale Galaxy Admins group](https://galaxyproject.org/community/sig/small-scale-admins/) is a [Galaxy community of practice](https://galaxyproject.org/community/sig/#communities-of-practice).
+The meetings are taking place every month and are listed in the [Galaxy WG calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com).

content/events/2025-02-small-scale/index.md

@@ -0,0 +1,25 @@
+---
+title: Small Scale Galaxy Admins Meeting
+date: '2025-02-20'
+days: 1
+continent: GL
+location:
+  name: Online, Global
+gtn: false
+contact:  Lucille Delisle, Hans-Rudolf Hotz
+tags:
+subsites: [all-eu, global, us]
+---
+
+
+
+Please <a href="https://epfl.zoom.us/j/69775900853?pwd=R1gzbllUZzg0RFUrM0Mzd2MvczE3Zz09">join us</a> 
+at 3 PM CET (<a href="https://www.timeanddate.com/worldclock/fixedtime.html?msg=Small+Scale+Galaxy+Admins+Meeting&iso=20250220T15&p1=945&ah=1">see in your timezone</a>) 
+for a discussion about general and current problems you encounter as a maintainer of a Galaxy server.
+
+
+
+---
+
+The [Small Scale Galaxy Admins group](https://galaxyproject.org/community/sig/small-scale-admins/) is a [Galaxy community of practice](https://galaxyproject.org/community/sig/#communities-of-practice).
+The meetings are taking place every month and are listed in the [Galaxy WG calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com).

content/events/gcc2024/sponsors/index.md

@@ -39,7 +39,7 @@ affordable and accessible.
 </a>
 
 <a href="https://www.kws.com/" target="_blank">
-  <img src="/images/logos/KWS-logo.jpg" alt="KWS" style="max-width: 25%; padding-right: 2rem;" />
+  <img src="/images/logos/kws-logo-slogan.png" alt="KWS" style="max-width: 25%; padding-right: 2rem;" />
 </a>
 
 <a href="https://www.limagrain.com/en" target="_blank">

content/events/gcc2024/training/metaproteomics/index.md

@@ -24,4 +24,4 @@ University of Minnesota
 
 ### Reid Wagner
 
-University of Minnesota
+University of Minnesota

content/ftp-upload/index.md

@@ -2,52 +2,40 @@
 title: Galaxy FTP Upload
 ---
 
-<div class="alert alert-success trim-p" role="alert">
-UPDATE: FTP upload is no longer supported on UseGalaxy.org. For more information and to learn about alternative options, please see https://help.galaxyproject.org/t/the-usegalaxy-org-ftp-service-will-be-decommissioned-on-august-12-2022/8318.
-</div>
-
 # File Upload via FTP
 
 Uploading data directly from the browser can be unreliable and cumbersome.
-Because of this some Galaxies including the [Main](/main/) allow you to upload data via FTP.
+Because of this some Galaxy instances allow you to upload data via FTP.
 FTP will allow you to monitor the upload status as well as resume interrupted transfers.
 Compression types .gz/.gzip, .bz/.bzip, .bz2/.bzip2, and single-file .zip are also supported.
 
+<div class="alert alert-info trim-p" role="alert">
+FTP upload is not supported on the usegalaxy.org instance.
+</div>
+
 ## Introduction
 
 If you are completely new to FTP transfers you might benefit from reading a [wikihow](https://www.wikihow.com/Use-FTP) page about it.
 
-To get started using FTP with Galaxy, you'll need to have registered a regular Galaxy account. Once registered, you can initiate an FTP connection in your preferred FTP
+To get started using FTP with Galaxy, you'll need to have registered a regular Galaxy account. If you are signed-in to Galaxy using a third-party identity and you do not have a Galaxy password please use the reset password option in the login form with your email to create a password for your account.
+
+Once you have a username and a password, you can initiate an FTP connection in your preferred FTP
 client. Please see the [comparison](https://en.wikipedia.org/wiki/Comparison_of_FTP_client_software) of available FTP clients.
 
 ## Upload with a client
 
-In this example, FileZilla for MacOS is used. Point your client to the FTP server hostname provided in the upload modal window (`usegalaxy.org` for Galaxy Main).
+In this example, FileZilla for MacOS is used. Point your client to the FTP server hostname provided in the upload modal window (e.g. `ftp.usegalaxy.eu` for Galaxy Europe).
 ![FTP client connection details](./ftp-connect.png)
 
-<div class="alert alert-warning trim-p" role="alert">
-
-If you are having trouble connecting to the [Main](/main/) server try enabling FTP with `passive` mode in your client. Please connect using `FTP`, `FTPS`, or `FTP-TLS` type of connections. All `SFTP` connections will be rejected.
-
-</div>
+If you are having trouble connecting to the server try enabling FTP with `passive` mode in your client.
 
 In most clients, when a connection is made with `FTP` or `FTPS`, a pop-up server certificate authentication will need to be accepted.
 
-<div class="embed-responsive embed-responsive-16by9">
-<iframe class="embed-responsive-item" src="https://player.vimeo.com/video/222236679?portrait=0" webkitallowfullscreen mozallowfullscreen allowfullscreen> </iframe>
-</div>
-
-In this video, the changes for `FTPS` are explained along with how to configure `FTP` client settings and verfify the target server's certificate.
-
-Below you can see my files copied to the destination on Galaxy's FTP server.
-![files uploaded to Galaxy FTP server](./ftp-files.png)
-
-Need more help? See: [Galaxy Help](https://help.galaxyproject.org/)
+For more help ask at [Galaxy Help](https://help.galaxyproject.org/).
 
+## Upload using command line
 
-
-## Upload with lftp (command line)
-
+### lftp
 In this example, `lftp` for MacOS is used.
 
 First, check to see if `lftp` is installed. Type in the command and the prompt will result, as show below, *if installed*. Type `exit` at the prompt to back out of the session.
@@ -59,26 +47,28 @@ lftp :~>
 
 If the command is not found, `brew` can be used to install `lftp`. [Instructions when using MacOS](http://macappstore.org/lftp/).
 
-Command-line for `lftp` when connecting to the Public Main Galaxy server. Executing the command will prompt for your password. Your `email` (aka `user@email.edu`) and `password` are exactly the same as when logging into your account at https://usegalaxy.org.
+Command-line for `lftp` when connecting to an example Galaxy server. Executing the command will prompt for your password. Your `email` (aka `user@email.example`) and `password` are exactly the same as when logging into your account at `https://usegalaxy.example`.
 
 For explicit FTPS:
 
 ```
-$ lftp -u user@email.edu usegalaxy.org
+$ lftp -u user@email.example ftp.usegalaxy.example
 ```
 
 For implicit FTPS:
 
 ```
-$ lftp -u user@email.edu ftps://usegalaxy.org
+$ lftp -u user@email.example ftps://ftp.usegalaxy.example
 ```
 
-If you are using a different Galaxy server, `FTPS` may or may not be enabled, or the server may only accept implicit or explicit `FTP/FTPS` connections. Check with the administrators of that server if you are not sure.
+On some Galaxy servers `FTPS` may or may not be enabled, or the server may only accept implicit or explicit `FTP/FTPS` connections. Check with the administrators of that server if you are not sure.
+
+### ftp
 
-General `FTP` instructions for a Galaxy server *that has `FTP` enabled but not `FTPS`*. The base URL for the server is used for `othergalaxy.org` in the command below. The `email` (aka `user@email.edu`) and `password` is also server specific and the same as when logging in through a browser.
+General `FTP` command for a Galaxy server *that has `FTP` enabled but not `FTPS`* is below. The `email` (aka `user@email.example`) and `password` is also server specific and the same as when logging in through a browser.
 
 ```
-$ ftp -u user@email.edu othergalaxy.org
+$ ftp -u user@email.example ftp.usegalaxy.example
 ```
 
 
@@ -88,13 +78,12 @@ Files uploaded to the FTP server won't automatically be imported to your history
 rather, you will be presented with a list of the contents of your FTP directory
 in the standard upload interface. Select the ones you want to import and hit Start.
 
-![FTP files on the Upload File tool form](./ftp-select.png)
+Depending on the configuration of your Galaxy the import dialogue will be either under `Upload -> Choose FTP Files` or `Upload -> Choose Remote Files -> FTP Directory`.
 
-<div class="alert alert-warning" role="alert">
-Files not imported within 3 days will be cleaned up from the FTP site.
+<div class="alert alert-info" role="alert">
+Files not imported within a couple of days are usually cleaned up from the FTP folder. Ask your Galaxy admin for details.
 </div>
 
-## Configure for your Galaxy
+## Configure your Galaxy as Admin
 
-FTP upload can be configured in local installations of Galaxy, instructions to do
-so can be found at [admin/config/upload-via-ftp](/admin/config/upload-via-ftp/).
+To configure FTP upload in your installations of Galaxy follow the instructions in the [admin documentation](https://docs.galaxyproject.org/en/master/admin/special_topics/ftp.html).

content/home/hero.md

@@ -2,7 +2,7 @@
 heading: Meet Galaxy
 notification: Galaxy Community Conference is behind us. <strong><a href="/events/gcc2024/" class="ml-2">See what happened.</a></strong>
 description: Meet Galaxy - <br>a data analysis universe
-image: <a href="/news/2024-05-29-galaxy-training-academy-call-contribution/"><img src="/images/splash/galaxy-training-accademy-banner.png" alt="Galaxy Training Academy"></a>
+image: <img src="/images/galaxy_logo_hub_white.svg" alt="Galaxy Community Hub logo">
 button1: Use Galaxy now
 button2: "Learn more: First Steps with Galaxy"
 buttonUrl2: /get-started/

content/home/research.yml

@@ -5,14 +5,14 @@ research1:
   content: "Galaxy can be installed locally, fine-tuned with a tailored toolset and no usage quotas."
   url: "https://www.zotero.org/groups/1732893/galaxy"
   links:
-  - title: "Hakimzadeh, Ali, et al. \"A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.\" Molecular Ecology Resources (2023)."
-    url: "https://doi.org/10.1111/1755-0998.13847"
-  - title: "Senft, Rebecca A., et al. \"A biologist’s guide to planning and performing quantitative bioimaging experiments.\" PLoS Biology 21.6 (2023): e3002167."
-    url: "https://doi.org/10.1371/journal.pbio.3002167"
-  - title: "Banh, Dalton V., et al. \"Bacterial cGAS senses a viral RNA to initiate immunity.\" Nature (2023): 1-8."
-    url: "https://doi.org/10.1038/s41586-023-06743-9"
-  - title: "Sokol-Borrelli, Sarah L., et al. \"A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease.\" Nature Communications 14.1 (2023): 6078."
-    url: "https://doi.org/10.1016/j.envint.2022.107531"
+  - title: "Dantan, L. et al. \"Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas\"  Sci Rep 14, 26914 (2024)"
+    url: "https://doi.org/10.1038/s41598-024-76096-4"
+  - title: "Yujing Ren et al. \"Effects of microplastics on litter decomposition in wetland soil\" Environmental Pollution, Volume 343, (2024)"
+    url: "https://doi.org/10.1016/j.envpol.2023.123145"
+  - title: "Mathieu-Bégné, E et al. \"Schistosoma haematobium and Schistosoma bovis first generation hybrids undergo gene expressions changes consistent with species compatibility and heterosis\" PLOS Neglected Tropical Diseases (2024)"
+    url: "https://doi.org/10.1371/journal.pntd.0012267"
+  - title: "Sarmah, P. et al. \"The functional and structural characterisation of the bZIP transcription factors from Myristica fragrans Houtt. associated to plant disease-resistant defence: An insight from transcriptomics and computational modelling\" International Journal of Biological Macromolecules, Vol 268, Part 2 (2024)"
+    url: "https://doi.org/10.1016/j.ijbiomac.2024.131817"
 
 research3:
   title: Popular tutorials
@@ -29,7 +29,6 @@ research3:
   - title: Quality Control
     url: "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html"
 
-
 research5:
   title: "Research highlights"
   content: "See how Galaxy cooperates and helps other projects. These are also great exemplars of how Galaxy is being used in production settings."