Merge pull request #21 from floradanna/user_guide

User guide
ELIXIR-Belgium · Mar 27, 2024 · 267b015 · 267b015
2 parents 0e875c0 + dfc55d2
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diff --git a/.travis.yml b/.travis.yml
diff --git a/Gemfile b/Gemfile
@@ -1,5 +1,5 @@
 source 'https://rubygems.org'
-ruby '2.7'
+ruby '2.7.7'
 
 gem 'github-pages'
 gem 'jekyll-sitemap'

diff --git a/Rakefile b/Rakefile
@@ -6,7 +6,7 @@ task :test do
   sh 'bundle exec jekyll build'
   options = {
     alt_ignore: [/.*/], # don't worry about images without an alt tag
-    url_ignore: [
+    ignore_urls: [
       /http(s)?:\/\/localhost.*/, # ignore links to localhost, which are shown when walking through the installation
       /https:\/\/www.nationalarchives.gov.uk.*/, 
       /https:\/\/bitbucket.org\/fairdom\/seek\/downloads\/seek*/,

diff --git a/_config.yml b/_config.yml
@@ -1,7 +1,7 @@
 #baseurl: /seek
 
-current_seek_version: "1.12.0"
-current_docker_tag: "1.12"
+current_seek_version: "1.14.2"
+current_docker_tag: "1.14"
 
 plugins:
   - jekyll-sitemap

diff --git a/_includes/head.html b/_includes/head.html
@@ -1,6 +1,6 @@
 <head>
     <meta charset="UTF-8">
-    <title>Seek4Science Docs - {{ page.title }}</title>
+    <title>FAIRDOM-SEEK Docs - {{ page.title }}</title>
 
     <link href="/images/favicon.png" rel="shortcut icon" type="image/png" />
     <meta name="viewport" content="width=device-width, initial-scale=1">
@@ -10,13 +10,12 @@
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/stylesheet.css" media="screen">
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/github-light.css" media="screen">
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/seek.css" media="screen">
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
+<!--    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>-->
 
     <!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
+    <script src="{{ site.baseurl }}/js/jquery/1.11.2/jquery.min.js"></script>
     <!-- Include all compiled plugins (below), or include individual files as needed -->
     <script src="{{ site.baseurl }}/js/bootstrap.min.js"></script>
 
-    {% include analytics.html %}
-    {% include cookie-popup.html %}
+
 </head>
diff --git a/contacting-us.md b/contacting-us.md
@@ -9,17 +9,9 @@ redirect_from: "/contacting_us.html"
 <!--We have a number of ways you can contact us:
 
 
-## Mailing lists
+## Contact FAIRDOM
 
-We have 2 Google Groups. These groups are open to anonymous queries, you don't have to be a group member to submit a query.
-
-* For technical or development related queries please use [SEEK Developers Group](http://groups.google.com/group/seek-developers)
-* For general queries, or queries about using SEEK please us [Seek4Science Group](http://groups.google.com/group/seek4science)
-
-
-## Contact form
-
-You can also contact us through [FAIRDOM](http://fair-dom.org) using our [Contact form](http://fair-dom.org/contact).
+You can contact us through [FAIRDOM](https://fair-dom.org) using [various channels](https://fair-dom.org/get_involved).
 
 This should be used if your query or feedback is of a more confidential nature. Remember to provide your email address.-->
 
@@ -33,5 +25,10 @@ Bugs and feature requests can be reported through [Github Issues](https://fair-d
 
 For more details and guidelines please visit [Reporting Bugs and raising Feature Requests](/tech/reporting-bugs-and-features.html)
 
+## Google groups
+
+We have 2 Google Groups. These groups are open to anonymous queries, you don't have to be a group member to submit a query.
 
+* For technical or development related queries please use [SEEK Developers Group](https://groups.google.com/group/seek-developers)
+* For general queries, or queries about using SEEK please us [Seek4Science Group](https://groups.google.com/group/seek4science)
 
diff --git a/contributing.md b/contributing.md
@@ -5,7 +5,7 @@ layout: page
 
 # Contributing
 
-We welcome many contributions to our [SEEK software](http://seek4science.org), these Documentation pages and our [FAIRDOM](http://fair-dom.org) project in general.
+We welcome many contributions to our [SEEK software](https://seek4science.org), these Documentation pages and our [FAIRDOM](https://fair-dom.org) project in general.
 
 Below are some guides for how you contribute to the software or these pages.
 

diff --git a/cookies.md b/cookies.md
@@ -11,4 +11,4 @@ Google Analytics records the pages you visited on the site, and information abou
 
 The information we gather from Google Analytics helps us measure which parts of the site are useful and popular, and which parts do not work so well. This allows us to tailor and improve the site for our visitors.
 
-You can learn more about [Google Analytics](http://www.google.com/analytics/learn/privacy.html), or if you wish to you can [Opt Out](https://tools.google.com/dlpage/gaoptout)
+You can learn more about [Google Analytics](https://www.google.com/analytics/learn/privacy.html), or if you wish to you can [Opt Out](https://tools.google.com/dlpage/gaoptout)
diff --git a/credits.md b/credits.md
@@ -9,29 +9,29 @@ layout: page
 
 * [WorkflowHub](https://about.workflowhub.eu/)
   - <https://workflowhub.eu/> is based on SEEK
-* [OpenBIS](http://fair-dom.org/platform/openbis/)
-* [BioVel](http://web.archive.org/web/20180202071633/http://www.biovel.eu/) (archived 2018-02-02)
-  - [BioVel portal](http://web.archive.org/web/20171112080623/https://portal.biovel.eu/) (archived 2017-11-12) was based on SEEK
+* [OpenBIS](https://openbis.ch/)
+* [BioVel](https://web.archive.org/web/20180202071633/http://www.biovel.eu/) (archived 2018-02-02)
+  - [BioVel portal](https://web.archive.org/web/20171112080623/https://portal.biovel.eu/) (archived 2017-11-12) was based on SEEK
 * [BiVeS](https://sems.uni-rostock.de/projects/bives/)
-* [SynBioChem](http://synbiochem.co.uk/)
+* [SynBioChem](https://synbiochem.co.uk/)
 * [Virtual Liver Network](http://www.virtual-liver.de/)
-* [myExperiment](http://www.myexperiment.org/)
-* [BioCatalogue](http://www.biocatalogue.org/)
+* [myExperiment](https://www.myexperiment.org/)
+* [BioCatalogue](https://esciencelab.org.uk/products/biocatalogue/)
 * [MethodBox](http://www.esciencelab.org.uk/products/methodbox/)
 
 ## External Services we use
 
-* [Sabio-RK](http://sabio.villa-bosch.de)
-* [CytoScape](http://cytoscapeweb.cytoscape.org)
-* [BioPortal](http://bioportal.bioontology.org)
-* [BioModels](http://www.ebi.ac.uk/biomodels-main/)
-* [JWS Online](http://jjj.biochem.sun.ac.za/)
-* [Pubmed](http://www.ncbi.nlm.nih.gov/pubmed)
-* [CrossRef](http://www.crossref.org/)
+* [Sabio-RK](http://sabio.h-its.org/)
+* [CytoScape](https://github.com/cytoscape/cytoscapeweb)
+* [BioPortal](https://bioportal.bioontology.org)
+* [BioModels](https://www.ebi.ac.uk/biomodels/)
+* [JWS Online](https://jjj.biochem.sun.ac.za/)
+* [Pubmed](https://pubmed.ncbi.nlm.nih.gov/)
+* [CrossRef](https://www.crossref.org/)
 
 ## Javascript tools
 
-* [FLOT plotting library](http://code.google.com/p/flot/)
+* [FLOT plotting library](https://code.google.com/p/flot/)
 * [Curved Lines plugin for FLOT](https://github.com/MichaelZinsmaier/CurvedLines)
 * [Pdf rendering library](https://github.com/mozilla/pdf.js)
 * [jScrollPane](http://jscrollpane.kelvinluck.com/)
@@ -46,18 +46,18 @@ HITS gGmbH.
 ## Icons and themes
 
 * Fairdom Logo: [Autumn Firefly Design](http://autumn-firefly.co.uk/)
-* [FamFamFam icon set (flags and silk)](http://www.famfamfam.com/lab/icons/silk/)
-* Institution icon: from [Icon Eden](http://web.archive.org/web/20150206235106/http://www.iconeden.com/) (archived 2015-02-06)
-* [Test Tube & Flask icons](http://www.clker.com/clipart-test-tube-icon.html) by OCAL on clker
-* [Crystal Clear Icon Set](http://www.iconarchive.com/show/crystal-clear-icons-by-everaldo.html) (LGPL)
-* [Organism Icon from IconIcon](http://iconicon.net/?page_id=79)
-* Zoom images from [Lightbox by Lokesh Dhakar](http://www.lokeshdhakar.com/projects/lightbox2/)
-* [Presentation icon](http://web.archive.org/web/20110508124549/http://www.mricons.com/icon/785/128/presentation-slides-icon) (archived 2011-05-08) by David Vignoni at Mr. Icons (LGPL)
-* [Strain image](http://en.wikipedia.org/wiki/File:Enterococcus_faecalis20023-300.jpg#file) from Wikimedia Commons
-* [expand plus icon](http://findicons.com/icon/439241/toggle_expand?id=439541) by Jack Cai, Creative Commons Attribution (by) 
-* [collapse minus icon](http://findicons.com/icon/439180/toggle_collapse?id=439440) by Jack Cai, Creative Commons Attribution (by)
+* [FamFamFam icon set (flags and silk)](https://github.com/legacy-icons/famfamfam-silk)
+* Institution icon: from [Icon Eden](https://web.archive.org/web/20150206235106/http://www.iconeden.com/) (archived 2015-02-06)
+* [Test Tube & Flask icons](https://www.clker.com/clipart-test-tube-icon.html) by OCAL on clker
+* [Crystal Clear Icon Set](https://www.iconarchive.com/show/crystal-clear-icons-by-everaldo.html) (LGPL)
+* [Organism Icon from IconIcon](https://iconicon.net/?page_id=79)
+* Zoom images from [Lightbox by Lokesh Dhakar](https://www.lokeshdhakar.com/projects/lightbox2/)
+* [Presentation icon](https://web.archive.org/web/20110508124549/http://www.mricons.com/icon/785/128/presentation-slides-icon) (archived 2011-05-08) by David Vignoni at Mr. Icons (LGPL)
+* [Strain image](https://en.wikipedia.org/wiki/File:Enterococcus_faecalis20023-300.jpg#file) from Wikimedia Commons
+* [expand plus icon](https://findicons.com/icon/439241/toggle_expand?id=439541) by Jack Cai, Creative Commons Attribution (by) 
+* [collapse minus icon](https://findicons.com/icon/439180/toggle_collapse?id=439440) by Jack Cai, Creative Commons Attribution (by)
 * Waiting icon from [FatCow Web Hosting](http://www.fatcow.com/)
-* [Font awesome](http://fortawesome.github.io/Font-Awesome/)
+* [Font awesome](https://github.com/FortAwesome/Font-Awesome)
 * [Fatcow icons set](http://www.fatcow.com/free-icons) (Creative Commons Attribution)
 
 ## scale images (To BE UPDATED)