initial materials

.gitignore

@@ -1,5 +1 @@
-_site/
-.sass-cache/
-.jekyll-cache/
-.jekyll-metadata
-Gemfile.lock
+.idea

README.md

@@ -1,12 +1,17 @@
-## About
+# ABLeS repository
 
-Please see the [How-to Guide for the template](https://australianbiocommons.github.io/how-to-guide-template/) for more information on how to get started.  
 
+# Acknowledgements
 
-## Acknowledgements for the guides
+This repository makes use of the ELIXIR toolkit theme:
 
-This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/), the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
+[![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
 
-This repository makes use of the ELIXIR toolkit theme: [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+# Other attributions
 
-This template is based on the [ELIXIR Toolkit Theme example](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme-example).
+## Building the site
+
+- [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+- [Adding an image caption](https://stackoverflow.com/a/30366422)
+- [CSS tutorial](https://www.w3schools.com/css/default.asp)
+- [just-the-docs](https://pmarsceill.github.io/just-the-docs/#getting-started)

_config.yml

@@ -1,36 +1,45 @@
-title: How-to Guide
-# This appears in the html browser tab for the site title (seen mostly by search engines, not users)
-
-#topnav_title: Website title
-# Optional: this appears on the top navigation bar next to the main_logo.svg icon
-
-description: "A bioinformatics focused How-to Guide"
-# Metadata description of the website
-
+# see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+title: ABLeS
+topnav_title: ABLeS
+description: ABLeS
 remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@1.26.0
+permalink: pretty
 
 theme_variables:
   # biocommons blue
   theme_color: 205a86
+  back_to_top: true
   topnav:
-    brand_logo: assets/img/logo_example.png
-
-exclude:
-  - README.md
-  - vendor
+    brand_logo: assets/img/main_logo.png
+    github: true
 
 defaults:
   -
     scope:
       path: ""
       type: "pages"
     values:
-      permalink: /:basename
       layout: "page"
       sidebar: main
 
-plugins:
-  - jemoji
-  - jekyll-sitemap
-  - jekyll-github-metadata
-  - webrick
+# Footer "Edit this page on GitHub" link text
+#gh_edit_link: true # show or hide edit this page link
+#gh_edit_link_text: "Edit this page on GitHub."
+#gh_edit_repository: "https://github.com/AustralianBioCommons/ables" # the github URL for your repo
+#gh_edit_branch: "main" # the branch that your docs is served from
+#gh_edit_view_mode: "tree" # "tree" or "edit" if you want the user to jump into the editor immediately
+
+# Enable or disable heading anchors
+#heading_anchors: true
+
+# Back to top link
+#back_to_top: true
+#back_to_top_text: "Back to top"
+
+# Aux links for the upper right navigation
+#aux_links:
+#  "View these docs on GitHub":
+#    - "https://github.com/AustralianBioCommons/ables/tree/main"
+
+# Makes Aux links open in a new tab. Default is false
+#aux_links_new_tab: true

_data/CONTRIBUTORS.yml

@@ -1,22 +1,76 @@
+# see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
 
-############################
-### List of contributors ###
-############################
+# List of contributors
+#
+# reference maintainers/contributors by their name used in contributors metadata section on the pages.
 
-### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+Steven Manos:
+    git: smanosmxm
+    email: steven@biocommons.org.au
+    orcid:
+    role: lead
+    affiliation: Australian BioCommons / University of Melbourne
 
-#############################################################################################################################################
-### add maintainers/contributors below and use their name in the contributors metadata section on each page they have contributed towards ###
-#############################################################################################################################################
+Johan Gustafsson:
+    git: supernord
+    email: johan@biocommons.org.au
+    orcid: 0000-0002-2977-5032
+    role: Engagement
+    affiliation: Australian BioCommons / University of Melbourne
 
-# an example contributor is included below
-# example roles include "lead", "first-author", "author", "editor", "workflow-tester"
+Ziad Al Bkhetan:
+    git: ziadbkh
+    email: ziad@biocommons.org.au
+    orcid: 0000-0002-4032-5331
+    role: Technical/Engagement
+    affiliation: Australian BioCommons / University of Melbourne
 
-#Johan Gustafsson:
-#    git: supernord
-#    email: johan@biocommons.org.au
-#    orcid: 0000-0002-2977-5032
-#    role: author
-#    affiliation: Australian BioCommons / University of Melbourne
+Hardip Patel:
+    git: hp2048
+    email: Hardip.patel@anu.edu.au
+    orcid: orcid=0000-0003-3169-049X
+    role: if89 Contributor
+    affiliation: National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University
 
+J King Chang:
+    git: JKing2000
+    email: joykchang@hotmail.com
+    orcid: 
+    role: if89 Contributor
+    affiliation: School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney
 
+Dale Roberts:
+    git: dsroberts
+    email: dsroberts@unimelb.edu.au
+    orcid: 0000-0003-3952-6344
+    role: if89 Contributor
+    affiliation: NCI (at the time of this work), ARC Centre of Excellence for Climate Extremes
+
+Andrey Bliznyuk:
+    git: 
+    email: Andrey.Bliznyuk@anu.edu.au
+    orcid: 
+    role: if89 Contributor
+    affiliation: NCI
+
+Kyle Drover:
+    git:  dorkylever
+    email: kyle.drover@anu.edu.au
+    orcid: 
+    role: if89 Contributor
+    affiliation: 
+
+
+Terry Bertozzi:
+    git: 
+    email: 
+    orcid: 0000-0001-6665-3395
+    role: if89 Contributor
+    affiliation: South Australian Museum
+
+Javed Shaikh:
+    git: 
+    email: javed.shaikh@anu.edu.au 
+    orcid: 
+    role: if89 Contributor
+    affiliation: NCI/ANU

_data/footer.yml

@@ -1,11 +1,7 @@
-# see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml
-copyright: Copyright notice
-extra_line:
+# see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
 columns:
-  - type: links
+  - type: image
+    image_width: 120px
     width: 3
-    children:
-      - url_text: Home
-        url: /
-      - url_text: Contributors
-        url: /contributors
+    src: 'assets/img/main_logo.png'
+    alt: Australian BioCommons logo

_data/sidebars/main.yml

@@ -1,8 +1,20 @@
+# see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
 subitems:
   - title: Home
     url: /index
-  - title: Example page
-    url: /example_page
-  - title: Contributors
-    url: /contributors
-
+  - title: ABLeS processes
+    url: /processes
+  - title: Available resources
+    url: /resources
+  - title: Community projects
+    url: /communities
+  - title: if89 repository
+    url: /if89
+  - title: Acknowledgements and authorship
+    url: /acknowledgements
+  - title: Help and contact details
+    url: /contact-us
+  - title: FAQ
+    url: /faq
+  - title: Team
+    url: /team

_sass/_bootstrap_variables.scss

@@ -1,25 +1,14 @@
-//
-// BioCommons Colors: https://github.com/AustralianBioCommons/umccr-dictionary/blob/main/docs/_sass/custom/custom.scss
-//
-
-$bioc-pink:#ed087c;
-$bioc-purple: #b21e8d;
-$bioc-blue: #205a86;
-$bioc-yellow: #f49f1d;
-$bioc-teal: #5ac3b1;
-$bioc-olive: #8ea869;
-$bioc-green: #2cb77c;
+/* see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme*/
 
 /*-----Theme colors-----*/
-$primary:       $bioc-blue;
-$secondary:     $bioc-teal;
+$primary:       #205a86;
+$secondary:     #5ac3b1;
 $light:         #f8f9fa;
-$blue:          $bioc-blue;
+$blue:          #205a86;
 $dark:          #212529;
 
 /*-----Custom values for Bootstrap variables-----*/
 $link-decoration: none;
-$navbar-light-hover-color: $primary;
+$nav-link-color: $dark;
+$nav-link-hover-color: $primary;
 $link-color: $blue;
-
-// Find out which bootstrap variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/bootstrap/_variables.scss

_sass/_custom_classes.scss

@@ -1,53 +1,24 @@
-// Include here all custom classes to add extra styling on top of what the theme and bootstrap variables offer. 
-
-//Example for highlighting the active page in the navigation:
-/*-----Top navigation-----*/
-
-.navbar-nav .nav-item > a {
-    &.active {
-        color: $white;
-        background-color: $primary;
-        border-radius: $border-radius;
-    }
-}
-
 /* see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme*/
 
 .navbar {
     .navbar-brand {
         font-size: 2.25rem;
-        color: $dark !important;
+        padding-top: 0;
+        padding-bottom: 0;
     }
 }
-
 img {
     @extend .img-fluid;
 }
 
-h2 {
-    padding-top: 10px;
-    display: block;
-    border-top: 1px solid $table-border-color;
-}
 
-/*-----Copied and adapted from https://github.com/elixir-europe/infectious-diseases-toolkit/blob/main/_sass/_custom_classes.scss-----*/
-/*-----Section navigation tiles-----*/
+.accordion-button:not(.collapsed) {
+ color:#FFFFFF;
+ background-color:#205a86;
+ box-shadow:inset 0 -1px 0 rgba(0,0,0,0.125)
+}
 
-.navigation-tiles {
-    .card:hover {
-        box-shadow: $box-shadow;
-    }
+.accordion-button {
+ background-color:#f8f9fa;
 
-    .card-header {
-        a:hover {
-            text-decoration: none;
-        }
-        h3 {
-            font-size: 1.2rem;
-        }
-    }
-    .card-text {
-        font-size: 0.9rem;
-    }
 }
-