Initial commit

.github/workflows/jekyll.yml

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+
+name: Jekyll site CI
+
+on:
+  pull_request:
+    branches: [ master, main ]
+
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.inputs.branch }}
+
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1.127.0
+        with:
+          ruby-version: '3.1'
+          bundler-cache: true
+          cache-version: 0
+
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v2
+
+      - name: Install dependencies
+        run: |
+          bundle install
+
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: |
+          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
+          JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1

.gitignore

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+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+Gemfile.lock

CITATION.cff

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+cff-version: 0.0.0
+message: "Please cite as below."
+authors:
+  - family-names: [family name goes here]
+    given-names: [given names go here]
+    orcid: [ORCID goes here]
+title: "Title of repository goes here"
+version: 0.0.0
+doi: [DOI goes here]
+date-released: YYYY-MM-DD

Gemfile

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+source "https://rubygems.org"
+
+group :jekyll_plugins do
+    gem "github-pages"
+  end

LICENSE

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+MIT License
+
+Copyright (c) 2022 ELIXIR Belgium
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+## About
+
+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 for the guides
+
+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).
+
+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)
+
+This template is based on the [ELIXIR Toolkit Theme example](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme-example).

_config.yml

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+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
+
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@1.26.0
+
+theme_variables:
+  # biocommons blue
+  theme_color: 205a86
+  topnav:
+    brand_logo: assets/img/logo_example.png
+
+exclude:
+  - README.md
+  - vendor
+
+defaults:
+  -
+    scope:
+      path: ""
+      type: "pages"
+    values:
+      permalink: /:basename
+      layout: "page"
+      sidebar: main
+
+plugins:
+  - jemoji
+  - jekyll-sitemap
+  - jekyll-github-metadata
+  - webrick

_data/CONTRIBUTORS.yml

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+
+############################
+### List of contributors ###
+############################
+
+### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+
+#############################################################################################################################################
+### add maintainers/contributors below and use their name in the contributors metadata section on each page they have contributed towards ###
+#############################################################################################################################################
+
+# an example contributor is included below
+# example roles include "lead", "first-author", "author", "editor", "workflow-tester"
+
+#Johan Gustafsson:
+#    git: supernord
+#    email: johan@biocommons.org.au
+#    orcid: 0000-0002-2977-5032
+#    role: author
+#    affiliation: Australian BioCommons / University of Melbourne
+
+

_data/affiliations.yml

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+############################
+### List of affiliations ###
+############################
+
+### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+
+#########################################################################################################
+### add affiliations below and use the name(s) in the relevant metadata sections or code on each page ###
+#########################################################################################################
+
+### add new affiliations below as needed
+
+- name: Australian BioCommons
+  image_url: /assets/img/main_logo.png
+  expose: true
+  type: infrastructure
+  url: https://www.biocommons.org.au/

_data/footer.yml

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+# see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml
+copyright: Copyright notice
+extra_line:
+columns:
+  - type: links
+    width: 3
+    children:
+      - url_text: Home
+        url: /
+      - url_text: Contributors
+        url: /contributors

_data/sidebars/main.yml

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+subitems:
+  - title: Home
+    url: /index
+  - title: Example page
+    url: /example_page
+  - title: Contributors
+    url: /contributors
+

_data/topnav.yml

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+## 
+## if you want to list an external url, use external_url instead of url. the theme will apply a different link base.
+subitems:
+- title: Home
+  url: /index
+

_sass/_bootstrap_variables.scss

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+//
+// 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;
+$bioc-green: #2cb77c;
+
+/*-----Theme colors-----*/
+$primary:       $bioc-blue;
+$secondary:     $bioc-teal;
+$light:         #f8f9fa;
+$blue:          $bioc-blue;
+$dark:          #212529;
+
+/*-----Custom values for Bootstrap variables-----*/
+$link-decoration: none;
+$navbar-light-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

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+// 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;
+    }
+}
+
+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-----*/
+
+.navigation-tiles {
+    .card:hover {
+        box-shadow: $box-shadow;
+    }
+
+    .card-header {
+        a:hover {
+            text-decoration: none;
+        }
+        h3 {
+            font-size: 1.2rem;
+        }
+    }
+    .card-text {
+        font-size: 0.9rem;
+    }
+}
+

_sass/_custom_variables.scss

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+// Find out which theme variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/_variables.scss
+// Copy paste theme here and change where necessary .

contributors.md

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+---
+title: Contributors
+toc: false
+---
+
+This How-to Guide would not be possible without the following contributors.
+
+{% include contributor-tiles-all.html %}

index.md

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+---
+title: How-to Guide landing page template
+type: template
+contributors: 
+description: Add a plain text description here.
+affiliations: 
+---
+
+
+## About 
+
+> Add 2-3 sentences here explaining the purpose of the specific guide you are creating.
+
+
+## Guide sections
+
+> You can use this section to add navigation tiles for the pages you have created as part of your guide.
+
+
+## Please cite this guide as follows
+
+> [Citation information goes here]
+
+
+## Acknowledgements
+
+> Don't delete anything from this section, only add.
+
+This guide makes use of the [ELIXIR toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+
+{% include image.html file="elixir-toolkit-theme_logo.svg" alt="Elixir Toolkit Theme logo" max-width="15em" %}
+
+## References
+
+> Add references as needed.
+