Merge pull request #2861 from mtangaro/master

Re-work ELIXIR-IT regional page

config.json

@@ -83,7 +83,7 @@
                 "name": "GenOuest"
             },
             "elixir-it": {
-                "name": "ELIXIR-IT/Laniakea"
+                "name": "ELIXIR-IT"
             },
             "ifb": {
                 "name": "ELIXIR-FR/IFB"

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>
+

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.
 

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!
 

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>

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:[email protected]">by mail</a>.

content/elixir-it/lower.md

@@ -0,0 +1 @@
+---

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>

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:[email protected]" 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>

content/elixir-it/main3.md

@@ -0,0 +1,29 @@
+---
+title: Galaxy Italy
+subtitle: Data policy
+---
+
+# Our Data Policy
+
+<table class="table table-striped">
+    <tr>
+      <th>Registered Users</th><th>Unregistered Users</th><th>GDPR Compliance</th>
+    </tr>
+    <tr>
+      <td>User data on UseGalaxy.it (i.e. datasets, histories) will be available as long as they are not deleted by the user.
+          Once marked as deleted the datasets will be permanently removed within 14 days. If the user "purges" the dataset in the
+          Galaxy, it will be removed immediately, permanently.
+          In special cases, an extended quota can be <a href="mailto:[email protected]" target="_blank">requested</a> 
+          for a limited time period..
+      </td>
+      <td>Processed data will only be accessible during one browser session, using a
+          cookie to identify your data. This cookie is not used for any other purposes
+          (e.g. tracking or analytics).
+          If UseGalaxy.it service is not accessed for 90 days, those datasets will be
+          permanently deleted.
+      </td>
+      <td>The Galaxy service complies with the EU General Data Protection Regulation
+          (GDPR). You can read more about this on our
+          <a href="https://www.recas-bari.it/index.php/en/recas-bari-users/elixir-documentation">Terms and Conditions</a>.</td>
+    </tr>
+</table>

content/elixir-it/main.md → content/elixir-it/main4.md

@@ -1,13 +1,18 @@
 ---
-title: Laniakea@ReCaS
+title: Galaxy Italy
+subtitle: Laniakea on-demand platform
 ---
 
+# Laniakea@ReCaS
+
 <div class="row">
 <div class="col-sm-6">
 
-The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks.
+The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster-backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks.
+
+For more information about Laniakea, please subscribe to our <a href="http://srv00.area.ba.cnr.it/mailman/listinfo/galaxy.elixir-ita.cnr.it">mailing list</a>.
 
-[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-secondary .trim-p}
+[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-primary .trim-p}
 
 </div>
 <div class="col-sm-6">

content/elixir-it/main5.md

@@ -0,0 +1,62 @@
+---
+title: Galaxy Italy
+subtitle: Laniakea on-demand platform
+---
+
+# Communities: Laniakea's public servers
+
+<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">Vinyl</h2>
+      <p class="card-text">VINYL (Variant prIoritizatioN bY survivaL analysis) integrates an innovative method for variant prioritization, along with a highly curated collection of databases and resources for the annotation of human genetic variants.</p>
+      <div class="text-center">
+          <br>
+          <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/branding/refs/heads/master/vinyl/Vinyl_logo.png" alt="Vinyl" height="100">
+          <br><br><br>
+          <a href="http://vinyl.cloud.ba.infn.it/galaxy" target="_top" class="btn btn-primary">Vinyl</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">CorGAT</h2>
+      <p class="card-text">CorGAT, the Coronavirus Genome Analysis Tool, is a novel, highly effective and user-friendly approach for the functional annotation of SARS-CoV-2 genomes based on Galaxy. </p>
+      <div class="text-center">
+        <br><br>
+        <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/branding/refs/heads/master/laniakea/laniakea_%40RECAS.png" alt="CorGAT" height="100">
+        <br><br><br>
+          <a href="http://corgat.cloud.ba.infn.it/galaxy" target="_top" class="btn btn-primary">CorGAT</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">ITSoneWB</h2>
+      <p class="card-text">ITSoneWB (ITSone WorkBench) collects and integrates the high-quality ITS1 reference collection in ITSoneDB with DNA metabarcoding well-established analysis pipelines and new tools in an easy-to-use service addressing the eukaryotic domain of life.</p>
+      <div class="text-center">
+        <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/branding/refs/heads/master/laniakea/laniakea_%40RECAS.png" alt="ITSoneWB" height="100">
+        <br><br><br>
+          <a href="http://itsonewb.cloud.ba.infn.it/galaxy" target="_top" class="btn btn-primary">ITSoneWB</a>
+      </div>
+    </div>
+  </div>
+</div>
+<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">PIPE-T</h2>
+      <p class="card-text">PIPE-T is the first Galaxy tool for parsing, filtering, normalising, imputing, and analysing RT-qPCR data. PIPE-T integrates the functionalities implemented in various R packages, such as HTqPCR, impute, and RankProd, in a simple, transparent, accessible, reproducible, and user-friendly environment.</p>
+      <div class="text-center">
+          <br>
+          <img src="https://raw.githubusercontent.com/Laniakea-elixir-it/branding/refs/heads/master/laniakea/laniakea_%40RECAS.png" alt="Vinyl" height="100">
+          <br><br>
+          <a href="http://igg.cloud.ba.infn.it/galaxy" target="_top" class="btn btn-primary">Pipe-T</a>
+      </div>
+    </div>
+  </div>
+  <div class="card border-white mb-1 mx-1" style="width: 18rem">
+  </div>
+  <div class="card border-white mb-1 mx-1" style="width: 18rem">
+  </div>
+</div>

content/elixir-it/navbar.yml

@@ -1,5 +1,6 @@
 style:
     color: "#2c81bb"
+    #lightBg: true
 left:
     - label: News
       relativeTo: subsite
@@ -8,7 +9,11 @@ left:
       relativeTo: subsite
       target: events/
     - label: People
-      target: https://usegalaxy-eu.github.io/elixir-it/people
+      relativeTo: subsite
+      target: people/
+    - label: Cite
+      relativeTo: subsite
+      target: cite/
 right:
     - label: Help
       contents:

content/elixir-it/news/main.md

@@ -1,5 +1,5 @@
 ---
-title: ELIXIR-IT/Laniakea Galaxy News
+title: Galaxy Italy News
 ---
 
 <img class="img-fluid float-right" src="/images/undraw-illustrations/news.svg" style="width:220px;" alt="news" />

content/elixir-it/people/index.md

@@ -0,0 +1,50 @@
+---
+title: Galaxy Italy Team
+---
+
+<div class="card-deck">
+
+  <div class="card" style="width: 18rem; padding: 1.5em .5em .5em; text-align: center">
+    <img src="https://avatars.githubusercontent.com/Federico77z" style="width: 45%; border-radius: 50%; margin: 0 auto; box-shadow: 0 0 10px rgba(0,0,0,.2)">
+    <div class="card-body">
+      <h4 class="card-title"><b>Federico Zambelli</b></h4>
+      <p class="card-text">ELIXIR-Italy technical coordinator and Galaxy Italy team leader</p>
+      <a href="mailto:[email protected]" title="Email"><i class="fa fa-envelope"></i></a>
+      <a href="https://github.com/Federico77z" title="GitHub"><i class="fa fa-github" aria-hidden="true"></i></a>
+      <a href="https://orcid.org/0000-0003-3487-4331"><i class="fab fa-orcid"></i></a>
+    </div>
+  </div>
+
+  <div class="card" style="width: 18rem; padding: 1.5em .5em .5em; text-align: center">
+    <img src="https://avatars.githubusercontent.com/mtangaro" style="width: 45%; border-radius: 50%; margin: 0 auto; box-shadow: 0 0 10px rgba(0,0,0,.2)">
+    <div class="card-body">
+      <h4 class="card-title"><b>Marco Antonio Tangaro</b></h4>
+      <p class="card-text">UseGalaxy.it and Laniakea lead developer</p>
+      <a href="mailto:[email protected]" title="Email"><i class="fa fa-envelope"></i></a>
+      <a href="https://github.com/mtangaro" title="GitHub"><i class="fa fa-github" aria-hidden="true"></i></a>
+      <a href="https://orcid.org/0000-0003-3923-2266"><i class="fab fa-orcid"></i></a>
+    </div>
+  </div>
+
+  <div class="card" style="width: 18rem; padding: 1.5em .5em .5em; text-align: center">
+    <img src="https://avatars.githubusercontent.com/LuigiMansi1" style="width: 45%; border-radius: 50%; margin: 0 auto; box-shadow: 0 0 10px rgba(0,0,0,.2)">
+    <div class="card-body">
+      <h4 class="card-title"><b>Luigi Mansi</b></h4>
+      <p class="card-text">UseGalaxy.it and Laniakea developer</p>
+      <a href="https://github.com/LuigiMansi1" title="GitHub"><i class="fa fa-github" aria-hidden="true"></i></a>
+    </div>
+  </div>
+
+  <div class="card" style="width: 18rem; padding: 1.5em .5em .5em; text-align: center">
+    <img src="https://avatars.githubusercontent.com/gm-ds" style="width: 45%; border-radius: 50%; margin: 0 auto; box-shadow: 0 0 10px rgba(0,0,0,.2)">
+    <div class="card-body">
+      <h4 class="card-title"><b>Gaetanomaria De Sanctis</b></h4>
+      <p class="card-text">UseGalaxy.it and Laniakea developer</p>
+      <a href="https://github.com/gm-ds" title="GitHub"><i class="fa fa-github" aria-hidden="true"></i></a>
+    </div>
+  </div>
+
+  <!--div class="card border-white mb-1 mx-1" style="width: 18rem; padding: 1.5em .5em .5em; text-align: center">
+  </div-->
+
+</div>