Hugo pathogens portal theme inspired by the Swedish Pathogens Portal
- Requirements
- Installation
- Customisation
- Menu
- Dashboards
- Events
- News
- Configuration
- Versioning
- Credits
- Contributing
- Hugo 0.124 or higher
Navigate to your hugo project root and run:
git submodule add https://github.com/sib-swiss/hugo-pathogens-portal themes/hugo-pathogens-portal
Then run hugo (or set theme = "hugo-pathogens-portal"/theme: hugo-pathogens-portal in configuration file)
hugo server --minify --theme hugo-pathogens-portal
You can also add this theme as a Hugo module instead of a git submodule.
Start with initializing hugo modules, if not done yet:
hugo mod init github.com/repo/path
Navigate to your hugo project root and add [module] section to your hugo.toml:
[module]
[[module.imports]]
path = 'github.com/sib-swiss/hugo-pathogens-portal'Then, to load/update the theme module and run hugo:
hugo mod get -u
hugo server --minifyBelow is an example on how to create a new site from scratch:
hugo new site myportal; cd myportal
git init
git submodule add https://github.com/sib-swiss/hugo-pathogens-portal themes/hugo-pathogens-portal
cp -R themes/hugo-pathogens-portal/exampleSite/content/* ./contenthugo server --minify --theme hugo-pathogens-portalTo add your own logo, create a static/images/portal.png file in your Hugo site. The logo will overwrite the default logo.
To add your own favicon, create a static/images/favicon.ico file in your Hugo site. The favicon will overwrite the default favicon.
The main menu is generated from the content files in the dashboards directory, the tags taxonomy, and the manually defined menu items.
Whenever you add a new content file in the dashboards directory, a new item will be added to the main menu.
Whenever you add a new tag to either a content file inside the dashboards directory or a content file in the news directory, a new item will be added to the main menu.
Finally, to add a new item to the menu, simply specify main in the front matter of the content file:
menu:
main:
name: "Research"
identifier: "research"If you wish that the menu item is expandable, you can use the identifier from the menu item as the parent identifier:
menu:
research:
name: "Infectious diseases"
identifier: "infectious-diseases"The navigation menu is display at the top right of the page.
To add entries to the navigation menu, you can add the following to the front matter of a content file:
menu:
navbar_top:
name: "About"
identifier: "about"The footer menu is displayed at the bottom of the page.
To add entries to the about section of the footer menu, you can add the following to the front matter of a content file:
menu:
footer_about:
name: "About"
identifier: "about"To add entries to the data section of the footer menu, you can add the following to the front matter of a content file:
menu:
footer_data:
name: "Data"
identifier: "data"Dashboards are displayed on the main page and can be filtered by tags.
To add a new dashboard, create a new markdown file in the content/dashboards directory. If you want to host the dashboard directly in your HUGO site, you will need to write the content of the dashboard in the markdown file. If you want to redirect to an external site, you can add the redirect_url parameter to the front matter of the markdown file.
Also, if you want to highlight a dashboard, you can add the highlight: true parameter to the front matter of the markdown file.
Finally, you can add tags to the dashboard by adding the tags parameter to the front matter of the markdown file.
---
title: "Infectious diseases dashboard"
description: "Information on cases of infection and illness in Switzerland and the Principality of Liechtenstein caused by various pathogens, provided by the Federal Office of Public Health."
image: dashboards/image.png
redirect_url: https://www.idd.bag.admin.ch/
highlight: true
tags:
- Surveillance
- Infectious diseases
---Events are displayed on the main page and can be filtered by categories.
To add a new event, create a new markdown file in the content/events directory.
Make sure to always add the following front matter to the markdown file:
---
title: "My event"
start_date: 2024-09-02T08:00:00Z
end_date: 2024-09-04T17:00:00Z
location: Geneva, Switzerland
description: This is a description of my event.
organiser: SIB Swiss Institute of Bioinformatics
external_url: https://www.sib.swiss/
categories:
- Training
- NGS
---Your events will then be automatically displayed on the main page. If the event is already over, it will be shown under the past events section.
News are displayed on the main page and can be filtered by tags.
To add a new news, create a new markdown file in the content/news directory.
Make sure to always add the following front matter to the markdown file:
---
title: "My news"
date: 2024-08-28T13:03:06+02:00
draft: false
author: "John Doe"
image: news/image.png
tags:
- COVID-19
---Keep in mind that the draft parameter is set to true by default. If you want to display the news on the main page, you will need to set it to false. Also, the date parameter is mandatory, if the date is in the future, the news will not be displayed.
You can configure the site by editing the config.toml file in the root of your Hugo site.
Here is an example configuration:
baseURL = "http://localhost/"
title = "Pathogens Portal"
theme = "hugo-pathogens-portal"
# (Optional) Set this to true to enable 'Last Modified by' date and git author
# information on 'doc' type pages.
# enableGitInfo = true
# Specify the default content language.
defaultContentLanguage = "en"
# Multilingual mode config
# There are different options to translate files
# See https://gohugo.io/content-management/multilingual/#translation-by-filename
# And https://gohugo.io/content-management/multilingual/#translation-by-content-directory
# [languages]
# [languages.en]
# languageName = "English"
# languageCode = "en"
# contentDir = "content"
# weight = 1
[params]
# (Optional) Set source repository location.
# Used for 'Last Modified' and 'Edit this page' links.
# repository = "https://github.com/sib-swiss/hugo-pathogens-portal"
# (Optional) Enable 'Edit this page' links for 'doc' page type.
# Disabled by default. Uncomment to enable. Requires 'BookRepo' param.
# Path must point to the site directory.
# editPath = 'edit/main/exampleSite'
# (Optional) Set the logo for your institution next to the pathogens-portal logo.
# logo = "images/logo.png"
# (Optional) Set the external link for the logo of your institution.
# homepage = "https://www.google.com"
# (Optional) Set the email to contact you
# mail = ""
# (Optional) Set the social media links for your institution.
# twitter = ""
# linkedin = ""
# (Optional) Set the country to retrieve stats from the central pathogens-portal.
# This is used to retrive several stats from the central pathogens-portal using the API
# and filtering by your configured country.
# country = "Switzerland"
# (Optional) Set the country to retrieve publications from the Europe PMC API.
# This is used to retrieve publications from the Europe PMC API and filtering by your configured country.
# pubmed_country = "Switzerland"
# (Optional) Set the URL of your national biobank to display the link on the homepage.
# biobank_url = ""Theme supports Hugo's multilingual mode, just follow configuration guide there.
This theme follows a simple incremental versioning. e.g. v1, v2 and so on. There might be breaking changes between versions.
If you want lower maintenance, use one of the released versions. If you want to live on the bleeding edge of changes, you can use the main branch and update your website when needed.
This theme is based on the Swedish Pathogens Portal (SciLifeLab Data Centre (2024) pathogens-portal v2.2.1) Zenodo, with funding from the BY-COVID project.
The source code of the Swedish Pathogens Portal is available on GitHub.
This theme is developed by the SIB Swiss Institute of Bioinformatics.
Contributions are welcome and will be fully credited. We accept contributions via Pull Requests on GitHub.
Feel free to open issues if you find missing configuration or customisation options.