Merge branch 'master' into deNBI-allhands-2024

galaxyproject · Jan 7, 2025 · a9e1bf4 · a9e1bf4
2 parents 722a569 + 8229aa2
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diff --git a/.github/workflows/links-internal.yml b/.github/workflows/links-internal.yml
@@ -18,7 +18,7 @@ jobs:
       - name: Get yarn cache directory path
         id: yarn-cache-dir-path
         run: echo "::set-output name=dir::$(yarn cache dir)"
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         id: yarn-cache
         with:
           path: ${{ steps.yarn-cache-dir-path.outputs.dir }}

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -12,7 +12,7 @@ jobs:
       - name: Get yarn cache directory path
         id: yarn-cache-dir-path
         run: echo "::set-output name=dir::$(yarn cache dir)"
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         id: yarn-cache # use this to check for `cache-hit` (`steps.yarn-cache.outputs.cache-hit != 'true'`)
         with:
           path: ${{ steps.yarn-cache-dir-path.outputs.dir }}

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -27,7 +27,7 @@ jobs:
         run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
 
       - name: Cache Yarn Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: yarn-cache
         with:
           path: ${{ steps.yarn-cache-dir-path.outputs.dir }}

diff --git a/config.json b/config.json
@@ -83,7 +83,7 @@
                 "name": "GenOuest"
             },
             "elixir-it": {
-                "name": "ELIXIR-IT/Laniakea"
+                "name": "ELIXIR-IT"
             },
             "ifb": {
                 "name": "ELIXIR-FR/IFB"

diff --git a/content/community/governance/gcb/index.md b/content/community/governance/gcb/index.md
@@ -33,18 +33,24 @@ You can learn more about **SIGs** in our dedicated tutorials below, or explore o
 
 <div style="text-align: center;">
   <div class="row">
-    <div class="col-md-6">
-      <div class="row">
-        <div style="border: 2px solid black; padding: 10px; margin: 5px;background-color: papayawhip">
+    <div class="col-md-12"> <!-- Changed from col-md-6 to col-md-12 -->
+      <div style="display: flex; flex-wrap: nowrap; justify-content: center;">
+        <div style="border: 2px solid black; padding: 10px; margin: 5px;background-color: papayawhip;">
           <a href="https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_define/tutorial.html">
-          <img src="gtn_hat.png" alt="GTN Hat" width="50">
-          What is a SIG?
+            <img src="gtn_hat.png" alt="GTN Hat" width="50">
+            What is a SIG?
           </a>
         </div>
-        <div style="border: 2px solid black; padding: 10px; margin: 5px;background-color: papayawhip">
+        <div style="border: 2px solid black; padding: 10px; margin: 5px;background-color: papayawhip;">
           <a href="https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_create/tutorial.html">
-          <img src="gtn_hat.png" alt="GTN Hat" width="50">
-          Creating a SIG
+            <img src="gtn_hat.png" alt="GTN Hat" width="50">
+            Creating a SIG
+          </a>
+        </div>
+        <div style="border: 2px solid black; padding: 10px; margin: 5px;background-color: papayawhip;">
+          <a href="https://training.galaxyproject.org/training-material/topics/community/faqs/governance_gcb_join.html">
+            <img src="gtn_hat.png" alt="GTN Hat" width="50">
+            Join the GCB
           </a>
         </div>
       </div>
@@ -68,6 +74,10 @@ from GEB and from GTB to be also members of the GCB. Therefore, it is recommende
 SIG members, and especially the representatives, are encouraged to join WG meetings or talk to WG representatives to raise issues or request help.
 For example, SIG members could request assistance from the tools and workflows WG. WGs might contact SIGs to collect feedback from the community.
 
+## Meetings Calendar
+
+<iframe src="https://calendar.google.com/calendar/embed?height=600&wkst=1&ctz=Europe%2FLondon&showPrint=0&mode=AGENDA&showCalendars=0&src=MDQwNDY2MDRhNGYxODE2NDk0MjBkYTQzMzUzMTBkN2E1MmQxMGJmNDkxNDgwMGEyZjNhYjEzZWE0ZWY3MzEyY0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t&color=%237CB342" style="border-width:0" width="800" height="600" frameborder="0" scrolling="no"></iframe>
+
 ## Origins
 
 During GCC 2023, we discussed how to empower the Galaxy community in terms of project planning, decision-making, execution, and overall governance. The Galaxy Community Board (GCB) was formed to take over from the Global Galaxy Steering Committee.
@@ -79,4 +89,4 @@ This page is brought to you by:
 with thanks for editing and review from:
 
  - [Saskia Hiltemann](https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/)
- - [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/)
+ - [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/)
diff --git a/content/community/governance/geb/index.md b/content/community/governance/geb/index.md
@@ -174,5 +174,6 @@ The GEB is a group of Galaxy advocates from around the world. It is currently (2
     * [Australian BioCommons](https://www.biocommons.org.au/), [The University of Queensland](https://www.uq.edu.au/), Australia
 * **[Bérénice Batut](https://research.bebatut.fr)**
     * [Institut Francais de Bioinformatique]([https://www.open.ac.uk/research/faculties](https://www.france-bioinformatique.fr/)), [AuBi](https://mesocentre.uca.fr/projets-associes/plateforme-aubi), France
-
+* **[Saskia Hiltemann](https://www.linkedin.com/in/shiltemann/)**
+    * [University of Freiburg](https://uni-freiburg.de/), Germany & The Netherlands
 <sup>*</sup> <small>But, well, obviously not.  Thank you Ross.</small>
diff --git a/content/community/sig/index.md b/content/community/sig/index.md
@@ -7,12 +7,18 @@ autotoc: false
 
 Active Galaxy communities are encouraged to participate in (or form) their own SIG, with a focus on specific shared interests. You can learn more in our dedicated tutorial: [What's a SIG?](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_define/tutorial.html)
 
-In the following you will find a list of current active Special Interest Groups. If you can't find yourself in this list we always welcome new SIGs.
-You can read more about the [GCB and SIGs](/community/governance/gcb/) or learn [how to set up your own](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_create/tutorial.html).
+# Galaxy Communities Calendar
+Check out the upcoming meetings across the communities.
+
+<iframe src="https://calendar.google.com/calendar/embed?height=600&wkst=1&ctz=Europe%2FLondon&showPrint=0&showCalendars=0&mode=AGENDA&src=OGE3NjI4OTBmYmU3MjRlOWQyOWI2NzkxNWFhMDE5N2EzNTI2NDJmOTRiMjJlYzY0YTg1NDMwZGFhZjFhYmI1ZUBncm91cC5jYWxlbmRhci5nb29nbGUuY29t&color=%234285F4" style="border-width:0" width="800" height="400" frameborder="0" scrolling="no"></iframe>
 
+*Please note: The Galaxy Community Board introduced this in December 2024, so we are still collecting communities to add to it! Do you not see your community? [Follow this FAQ](https://training.galaxyproject.org/training-material/topics/community/faqs/community_activites_calendar.html) to add it!*
 
 # Directory of Special Interest Groups
 
+In the following you will find a list of current active Special Interest Groups. If you can't find yourself in this list we always welcome new SIGs.
+You can read more about the [GCB and SIGs](/community/governance/gcb/) or learn [how to set up your own](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_create/tutorial.html).
+
 ---
 
 ## Communities of Practice

diff --git a/content/community/sig/singlecell/index.md b/content/community/sig/singlecell/index.md
@@ -68,14 +68,9 @@ Our meeting agenda is:
 
 # How can you join & other important links
 
-Start by joining our <i class="fa fa-coffee" aria-hidden="true"></i> [🖖🏾SPOC Chatroom](https://matrix.to/#/#spoc3:matrix.org) and introduce yourself! (Or you can just lurk there for a bit!)
-
- - <i class="fa fa-envelope" aria-hidden="true"></i>&nbsp;&nbsp;   [Mailing list](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/)
- - <i class="fa fa-trello" aria-hidden="true"></i>&nbsp;&nbsp; [ClickUp site](https://sharing.clickup.com/9015477668/b/h/5-90152810734-2/557452707486fef) & [Sign-up to edit](https://forms.gle/TgCyHMiBcwFBskef6)
- - <i class="fa fa-calendar" aria-hidden="true"></i>&nbsp;&nbsp; [🖖🏾SPOC Google Calendar](https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ctz=Europe%2FLondon)
- - <i class="fa fa-calendar" aria-hidden="true"></i>&nbsp;&nbsp; [🖖🏾SPOC iCalendar for non-google users](https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/basic.ics)
- - <i class="fa fa-list-alt" aria-hidden="true"></i>&nbsp;&nbsp; [Meeting Notes doc](https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtfmHSA/edit?usp=sharing) <--- There's a section here called 'New here?' that gives tips on how to start contributing as well!
- - <i class="fa fa-comments-o" aria-hidden="true"></i>&nbsp;&nbsp; [User Matrix Channel](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im)
+1. Start by joining our <i class="fa fa-coffee" aria-hidden="true"></i> [🖖🏾SPOC Chatroom](https://matrix.to/#/#spoc3:matrix.org) and introduce yourself! (Or you can just lurk there for a bit!)
+
+2. Then, follow the instructions on our ['👋🏾New here?'](https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtfmHSA/edit?tab=t.34ufduimwwz5) tab for key links to calendars, notes, how to contribute, and more!
 
 ## Key words
 

diff --git a/content/elixir-it/cite/index.md b/content/elixir-it/cite/index.md
@@ -0,0 +1,61 @@
+---
+title: Cite us
+---
+
+<h3><strong>If UseGalaxy.it and/or Laniakea helped you, please do not forget to cite us.</strong></h3>
+<br>
+
+<h4>Publications</h4>
+
+<div>
+
+<h2 class="bibliography">2024</h2>
+<ol class="bibliography">
+
+<li><span id="laniakea_dashboard_2024">Tangaro,M.A. <i>et al.</i> (2024) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. <i>NAR Genomics and Bioinformatics, 2024, 6(4), lqae140</i>.</span><a href="https://doi.org/10.1093/nargab/lqae140"> DOI: 10.1093/nargab/lqae140</a>.</li>
+<br>
+<li><span id="galaxy_2024">The Galaxy Community (2024) The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update <i>Nucleic Acids Research, 2024, 52(W1), pp. W83–W94</i>.</span><a href="https://doi.org/10.1093/nar/gkae410"> DOI: 10.1093/nar/gkae410</a>.</li>
+</ol>
+
+
+<h2 class="bibliography">2023</h2>
+<ol class="bibliography">
+<li><span id="laniakea_dashboard_2023">Tangaro,M.A. <i>et al.</i> (2023) The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. <i>Communications in Computer and Information Science, 2023, 1668 CCIS, pp. 179–191</i>.</span><a href="https://doi.org/10.1007/978-3-031-25380-5_14"> DOI: 10.1007/978-3-031-25380-5_14</a>.</li>
+<br>
+<li><span id="mandreoli_rcasc_2023">Mandreoli,P. <i>et al.</i> (2023) Using “Galaxy-rCASC”: A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis. <i>Methods in Molecular Biology, 2023, 2584, pp. 311–335</i>.</span><a href="https://doi.org/10.1007/978-1-0716-2756-3_16"> DOI: 10.1007/978-1-0716-2756-3_16</a>.</li>
+</ol>
+
+
+<h2 class="bibliography">2022</h2>
+<ol class="bibliography">
+<li><span id="galaxy_2022">The Galaxy Community (2024) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update <i>Nucleic Acids Research, 2022, 50(W1), pp. W345–W351</i>.</span><a href="https://doi.org/10.1093/nar/gkac247"> DOI: 10.1093/nar/gkac247</a>.</li>
+</ol>
+
+
+<h2 class="bibliography">2021</h2>
+<ol class="bibliography">
+<li><span id="laniakea_recas">Tangaro,M.A. <i>et al.</i> (2021) Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. <i>BMC Bioinformatics, 2021, 22, 544</i>.</span><a href="https://doi.org/10.1186/s12859-021-04401-3"> DOI: 10.1186/s12859-021-04401-3</a>.</li>
+<br>
+<li><span id="ascan">Zambelli,F. <i>et al.</i> (2021) aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals. <i>Journal of Molecular Biology, 2021, 433(11), 166829</i>.</span><a href="https://doi.org/10.1016/j.jmb.2021.166829"> DOI: 10.1016/j.jmb.2021.166829</a>.</li>
+
+</ol>
+
+
+<h2 class="bibliography">2020</h2>
+<ol class="bibliography">
+<li><span id="vinyl">Chiara,M. <i>et al.</i> (2020) VINYL: Variant prIoritizatioN by survivaL analysis. <i>Bioinformatics, 2020, 36(24), pp. 5590–5599</i>.</span><a href="https://doi.org/10.1093/bioinformatics/btaa1067"> DOI: 10.1093/bioinformatics/btaa1067</a>.</li>
+<br>
+<li><span id="corgat">Chiara,M. <i>et al.</i> (2020) CorGAT: A tool for the functional annotation of SARS-CoV-2 genomes. <i>Bioinformatics, 2020, 36(22-23), pp. 5522–5523</i>.</span><a href="https://doi.org/10.1093/bioinformatics/btaa1047"> DOI: 10.1093/bioinformatics/btaa1047</a>.</li>
+<br>
+<li><span id="hpc_at_cineca">Castrignanò,T. <i>et al.</i> (2020) ELIXIR-IT HPC@CINECA: High performance computing resources for the bioinformatics community. <i>BMC Bioinformatics, 2020, 21, 352</i>.</span><a href="https://doi.org/10.1186/s12859-020-03565-8"> DOI: 10.1186/s12859-020-03565-8</a>.</li>
+<br>
+<li><span id="laniakea_2020">Tangaro,M.A. <i>et al.</i> (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. <i>GigaScience, 2020, 9(4), giaa033</i>.</span><a href="https://doi.org/10.1093/gigascience/giaa033"> DOI: 10.1093/gigascience/giaa033</a>.</li>
+</ol>
+
+
+<h2 class="bibliography">2019</h2>
+<ol class="bibliography">
+<li><span id="pipet">Zanardi,N. <i>et al.</i> (2019) PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data. <i>Scientific Reports, 2019, 9(1), 17550</i>.</span><a href="https://doi.org/10.1038/s41598-019-53155-9"> DOI: 10.1038/s41598-019-53155-9</a>.</li>
+</ol>
+</div>
+
diff --git a/content/elixir-it/events/archive/main.md b/content/elixir-it/events/archive/main.md
@@ -1,6 +1,6 @@
 ---
-title: ELIXIR-IT/Laniakea Galaxy Event Archive
+title: Galaxy Italy Event Archive
 ---
 
-Old events relevant to the ELIXIR-IT/Laniakea Galaxy community.
+Old events relevant to the Italian Galaxy community.
 
diff --git a/content/elixir-it/events/main.md b/content/elixir-it/events/main.md
@@ -1,10 +1,10 @@
 ---
-title: ELIXIR-IT/Laniakea Event Horizon
+title: Galaxy Italy Event Horizon
 ---
 
 <img class="img-fluid float-right" src="/images/undraw-illustrations/events.svg" style="width:220px;" alt="events" />
 
-Upcoming (and past) events with content relevant to the ELIXIR-IT/Laniakea Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/).
+Upcoming (and past) events with content relevant to the Italian Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/).
 
 ### Advertise your event!
 

diff --git a/content/elixir-it/lead.md → content/elixir-it/lead.md.off b/content/elixir-it/lead.md → content/elixir-it/lead.md.off
diff --git a/content/elixir-it/lead1.md b/content/elixir-it/lead1.md
@@ -0,0 +1,8 @@
+<div class="center">
+
+<div class="img-sizer center" style="height: 200px">
+
+[![](/images/logos/usegalaxy-it.png)](https://usegalaxy.it)
+
+</div>
+</div>
diff --git a/content/elixir-it/lead2.md b/content/elixir-it/lead2.md
@@ -0,0 +1,3 @@
+**Galaxy** is a user-friendly open-source web platform designed to facilitate accessible, reproducible, and transparent computational research. It provides access to a vast collection of free-to-use, well-documented and maintained tools.
+
+**Galaxy Italy** provides Elixir Italy users and beyond compute and storage resources for running several tools in different research domains. For more information, issues and suggestions please contact us <a href="mailto:usegalaxy@elixir-ita.cnr.it">by mail</a>.
diff --git a/content/elixir-it/lower.md b/content/elixir-it/lower.md
@@ -0,0 +1 @@
+---
diff --git a/content/elixir-it/lower1.md → content/elixir-it/lower1.md.off b/content/elixir-it/lower1.md → content/elixir-it/lower1.md.off
diff --git a/content/elixir-it/lower2.md → content/elixir-it/lower2.md.off b/content/elixir-it/lower2.md → content/elixir-it/lower2.md.off
diff --git a/content/elixir-it/main1.md b/content/elixir-it/main1.md
@@ -0,0 +1,11 @@
+---
+title: Galaxy Italy
+subtitle: The homepage of the Italian Galaxy community
+---
+<div class="card border-secondary bg-secondary" style="width: 100%;">
+  <div class="card-body">
+    <h2 class="card-title text-dark">The Italian Galaxy server</h2>
+    <p class="card-text">The Italian Galaxy server UseGalaxy.it is maintained primarily by ELIXIR-ITALY, in collaboration with many academic groups across Italy. Please check our <a href="https://www.recas-bari.it/index.php/en/recas-bari-users/elixir-documentation">Terms of Use</a> before using the server.</p>
+    <p class="card-text">The following Institutions are actively providing resource to usegalaxy.it: CNR, INFN, University of Bari, Consortium GARR, CINECA and University of Milan.</p>
+  </div>
+</div>
diff --git a/content/elixir-it/main2.md b/content/elixir-it/main2.md
@@ -0,0 +1,67 @@
+---
+title: Galaxy Italy
+subtitle: The homepage of the Italian Galaxy community
+---
+
+<!-- Color palette: https://www.color-hex.com/color-palette/9983 -->
+<!-- Projects/Communities/Citation/Team cards -->
+
+<div class="card-deck">
+  <div class="card border-secondary bg-light mb-1 mx-1" style="width: 18rem">
+    <div class="card-body">
+      <h2 class="card-title text-dark">Contact</h2>
+      <p class="card-text">Ask for help, tools, or temporary increase of quota on our support forum</p>
+      <div class="text-center">
+          <img src="/images/undraw-illustrations/questions.svg" alt="qsupport" height="100">
+          <br><br><br><br>
+          <a href="mailto:usegalaxy@elixir-ita.cnr.it" class="btn btn-primary">Contact support</a>
+      </div>
+    </div>
+  </div>
+  <div class="card border-secondary bg-light mb-1 mx-1" style="width: 18rem">
+    <div class="card-body">
+      <h2 class="card-title text-dark">Get information</h2>
+      <p class="card-text">Be updated on the Italian Galaxy community activities! Subscribe to our mailing list.</p>
+      <div class="text-center">
+        <img src="/images/undraw-illustrations/newsletter.svg" alt="training" height="100">
+        <br><br><br>
+        <a href="http://srv00.area.ba.cnr.it/mailman/listinfo/galaxy.elixir-ita.cnr.it" class="btn btn-primary">Newsletter</a>
+      </div>
+    </div>
+  </div>
+  <div class="card border-secondary bg-light mb-1 mx-1" style="width: 18rem">
+    <div class="card-body">
+      <h2 class="card-title text-dark">Laniakea</h2>
+      <p class="card-text">Need to deploy your own Galaxy instance? Have a look to Laniakea.</p>
+      <div class="text-center">
+        <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/branding/refs/heads/master/laniakea/laniakea_logo_def.png" alt="Laniakea" height="100">
+        <br><br><br><br>
+        <a href="https://laniakea-elixir-it.github.io/" class="btn btn-primary">Get access</a>
+      </div>
+    </div>
+  </div>
+  <div class="card border-secondary bg-light mb-1 mx-1" style="width: 18rem">
+    <div class="card-body">
+      <h2 class="card-title text-dark">Citation</h2>
+      <p class="card-text">Have you used the Italian Galaxy server or Laniakea for your data analysis?</p>
+      <br>
+      <div class="text-center">
+        <img src="/images/undraw-illustrations/citations.svg" alt="citation" height="100">
+        <br><br><br>
+        <a href="/elixir-it/cite" class="btn btn-primary">Cite us!</a>
+      </div>
+    </div>
+  </div>
+  <div class="card border-secondary bg-light mb-1 mx-1" style="width: 18rem">
+    <div class="card-body">
+      <h2 class="card-title text-dark">Elixir Italy</h2>
+      <p class="card-text">For any questions regarding ELIXIR-Italy initiatives, please contact us.</p>
+      <br><br>
+      <div class="text-center">
+        <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/resources/master/logos/elixir_italy_white_background.png" alt="team" height="100">
+        <br><br>
+        <a href="https://elixir-italy.org" class="btn btn-primary" target="_blank">Web site</a>
+      </div>
+    </div>
+  </div>
+</div>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		Galaxy is a user-friendly open-source web platform designed to facilitate accessible, reproducible, and transparent computational research. It provides access to a vast collection of free-to-use, well-documented and maintained tools.

		Galaxy Italy provides Elixir Italy users and beyond compute and storage resources for running several tools in different research domains. For more information, issues and suggestions please contact us <a href="mailto:usegalaxy@elixir-ita.cnr.it">by mail</a>.