Merge branch 'master' into in-out

.gitignore

@@ -15,3 +15,4 @@ vendor
 *.swp
 .jekyll-metadata
 .jekyll-cache
+plantuml.jar

CONTRIBUTORS.yaml

@@ -138,7 +138,7 @@ cganote:
     name: Carrie Ganote
 
 chrisbarnettster:
-    name: Christopher Barnettster
+    name: Christopher Barnett
     gitter: chrisbarnettster
 
 daltis20012009:
@@ -205,7 +205,11 @@ fidelram:
     name: Fidel Ramirez
 
 foellmelanie:
-    name: Melanie Foell
+    name: Melanie Föll
+    email: melanie.foell@mol-med.uni-freiburg.de
+    twitter: MCFoell
+    gitter: foellmelanie
+    orcid: 0000-0002-1887-7543
 
 fpsom:
     name: Fotis E. Psomopoulos
@@ -346,7 +350,7 @@ marziacremona:
     email: mac78@psu.edu
 
 matthias313:
-    name: Matthias
+    name: Matthias Fahrner
 
 mblue9:
     name: Maria Doyle
@@ -402,6 +406,10 @@ NickSto:
     name: Nick Stoler
     twitter: NickStoler
 
+nomadscientist:
+    name: Wendi Bacon
+    email: wendi@ebi.ac.uk
+
 nsoranzo:
     name: Nicola Soranzo
     gitter: nsoranzo
@@ -496,8 +504,8 @@ subinamehta:
     linkedin: subinamehta
     gitter: subinamehta
     orcid: 0000-0001-9818-0537
-    
-    
+
+
 tealiie:
 
 thomasmanke:
@@ -540,7 +548,7 @@ tklingstrom:
     twitter: tklingstrom
     gitter: tklingstrom
     orcid: 0000-0002-9504-1352
-    
+
 valentinmarcon:
     name: Valentin Marcon
 

Makefile

@@ -31,7 +31,7 @@ endif
 default: help
 
 install-conda: ## install Miniconda
-	curl $(MINICONDA_URL) -o miniconda.sh
+	curl -L $(MINICONDA_URL) -o miniconda.sh
 	bash miniconda.sh -b
 .PHONY: install-conda
 

_config.yml

@@ -79,80 +79,76 @@ scholar:
 
 # Icon tag config
 icon-tag:
-  # in tutorials
-  question: fa-question-circle
-  solution: fa-eye
-  hands_on: fa-pencil
-  comment: fa-commenting-o
-  tip: fa-lightbulb-o
-  objectives: fa-bullseye
-  requirements: fa-check-circle
-  time: fa-hourglass-end
-  keypoints: fa-key
-  tool: fa-wrench
-  workflow: fa-project-diagram
-  feedback: fa-comments-o
-  congratulations: fa-thumbs-up
-  trophy: fa-trophy
-  warning: fa-warning
-  details: fa-info-circle
-  exchange: fa-exchange
-  wf-input: fa-chevron-circle-right
-  sticky-note: fa-sticky-note
-  new-history: fa-plus
-  param-file: fa-file-o
-  param-files: fa-files-o
-  param-collection: fa-folder-o
-  param-text: fa-pencil
-  param-check: fa-check-square-o
-  param-select: fa-filter
-  param-repeat: fa-plus-square-o
-  galaxy-eye: fa-eye
-  galaxy-info: fa-info-circle
-  galaxy-gear: fa-cog
-  galaxy-history: fa-archive
-  galaxy-library: fa-folder
-  galaxy-pencil: fa-pencil
-  galaxy-refresh: fa-refresh
-  galaxy-barchart: fa-bar-chart
-  galaxy-cross: fa-times
-  galaxy-columns: fa-columns
-  galaxy-tags: fa-tags
-  galaxy-selector: fa-check-square-o
-  galaxy-upload: fa fa-upload
-  galaxy-chart-select-data: fa fa-database
-  galaxy-save: fa fa-save
-  galaxy-scratchbook: fa fa-th
-  galaxy-dropdown: fa-caret-down
-  workflow-runtime-toggle: fa-caret-square-o-up
-  galaxy-wf-connection: fa-arrows-h
-  galaxy-wf-new: fa-plus
-  search: fa fa-search
   code-in: far fa-keyboard
   code-out: fas laptop-code
-
-  # menus, links
-  zenodo_link: fa-files-o
-  tutorial: fa-laptop
-  slides: fa-slideshare
-  interactive_tour: fa-magic
-  workflow: fa-share-alt
-  topic: fa-folder-o
-  instances: fa-globe
-  docker_image: fa-ship
-  galaxy_instance: fa-external-link
-  last_modification: fa-calendar
-  references: fa-bookmark
-  gitter: fa-comments
-  help: fa-life-ring
-  github: fa-github
-  email: fa-envelope-o
-  twitter: fa-twitter
-  linkedin: fa-linkedin
-  orcid: ai-orcid
-  curriculum: fa-graduation-cap
-  level: fa-graduation-cap
-  hall-of-fame: fa-users
+  comment: far fa-comment-dots
+  congratulations: far fa-thumbs-up
+  curriculum: fas fa-graduation-cap
+  details: fas fa-info-circle
+  docker_image: fab fa-docker
+  email: far fa-envelope
+  exchange: fas fa-exchange-alt
+  feedback: far fa-comments
+  galaxy-barchart: fas fa-chart-bar
+  galaxy-chart-select-data: fas fa-database
+  galaxy-columns: fas fa-columns
+  galaxy-cross: fas fa-times
+  galaxy-dropdown: fas fa-caret-down
+  galaxy-eye: far fa-eye
+  galaxy-gear: fas fa-cog
+  galaxy-history: fas fa-columns
+  galaxy-info: fas fa-info-circle
+  galaxy-library: far fa-folder
+  galaxy-pencil: fas fa-pencil-alt
+  galaxy-refresh: fas fa-sync-alt
+  galaxy-save: far fa-save
+  galaxy-scratchbook: fas fa-th
+  galaxy-selector: far fa-check-square
+  galaxy-tags: fas fa-tags
+  galaxy-upload: fas fa-upload
+  galaxy-wf-connection: fas fa-arrows-alt-h
+  galaxy-wf-new: fas fa-plus
+  galaxy_instance: fas fa-external-link-alt
+  github: fab fa-github
+  gitter: fab fa-gitter
+  hall-of-fame: fas fa-users
+  hands_on: fas fa-pencil-alt
+  help: far fa-question-circle
+  instances: fas fa-globe
+  interactive_tour: fas fa-magic
+  keypoints: fas fa-key
+  last_modification: far fa-calendar
+  level: fas fa-graduation-cap
+  linkedin: fab fa-linkedin
+  new-history: fas fa-plus
+  objectives: fas fa-bullseye
+  orcid: fab fa-orcid
+  param-check: far fa-check-square
+  param-collection: far fa-folder
+  param-file: far fa-file
+  param-files: far fa-copy
+  param-repeat: far fa-plus-square
+  param-select: fas fa-filter
+  param-text: fas fa-pencil-alt
+  question: far fa-question-circle
+  references: far fa-bookmark
+  requirements: fas fa-check-circle
+  search: fas fa fa-search
+  slides: fab fa-slideshare
+  solution: far fa-eye
+  sticky-note: fas fa-sticky-note
+  time: fas fa-hourglass-half
+  tip: far fa-lightbulb
+  tool: fas fa-wrench
+  topic: far fa-folder
+  trophy: fas fa-trophy
+  tutorial: fas fa-laptop
+  twitter: fab fa-twitter
+  warning: fas fa-exclamation-triangle
+  wf-input: fas fa-chevron-circle-right
+  workflow-runtime-toggle: far fa-caret-square-up
+  workflow: fas fa-share-alt
+  zenodo_link: far fa-copy
 
 # To exclude in _site
 exclude:

_layouts/base.html

@@ -13,7 +13,7 @@
         <link rel="stylesheet" href="{{ "/assets/css/bootstrap.min.css?v=3" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/bootstrap-toc.min.css" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/main.css?v=2" | prepend: site.baseurl }}">
-        <link rel="stylesheet" href="{{ "/assets/css/font-awesome.css" | prepend: site.baseurl }}">
+        <script src="https://kit.fontawesome.com/67b3f98409.js" crossorigin="anonymous"></script>
         <link rel="stylesheet" href="{{ "/assets/css/academicons.css" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/syntax_highlighting.css" | prepend: site.baseurl }}">
         <link rel="shortcut icon" href="{{ "/favicon.ico" | prepend: site.baseurl }}" type="image/x-icon" />

_layouts/base_slides.html

@@ -16,7 +16,7 @@
         {% include _includes/analytics.html %}
     {% endif %}
     <link rel="stylesheet" href="{{ "/assets/css/slides.css" | prepend: site.baseurl }}">
-    <link rel="stylesheet" href="{{ "/assets/css/font-awesome.css" | prepend: site.baseurl }}" id="theme">
+    <script src="https://kit.fontawesome.com/67b3f98409.js" crossorigin="anonymous"></script>
     <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="shortcut icon" href="{{ "/favicon.ico" | prepend: site.baseurl }}" type="image/x-icon" />
 

_plugins/jekyll-icon-tag.rb

@@ -18,7 +18,7 @@ def render(context)
       end
 
       if icon.start_with?("fa")
-          %Q(<i class="fa #{icon}" aria-hidden="true"></i><span class="visually-hidden">#{@text}</span>)
+          %Q(<i class="#{icon}" aria-hidden="true"></i><span class="visually-hidden">#{@text}</span>)
       elsif icon.start_with?("ai")
           %Q(<i class="ai #{icon}" aria-hidden="true"></i><span class="visually-hidden">#{@text}</span>)
       end