biouno/biouno.github.io

BioUno web site

BioUno.org

BioUno website.

Building

You must install Hugo to build the project locally. The Hugo website contains information to install it on Linux, macOS, and Windows. Hugo is written in Go, so you will have to install Go as well — refer to Hugo website.

Go into the directory where you cloned this repository, and run Hugo to build or to serve the website locally.

# This will build
$ hugo

# This will serve and watch for changes
$ hugo server --watch

If you want to have a more verbose output, you can use this variation.

$ hugo server --navigateToChanged --buildDrafts --buildFuture --watch --verbose

And if you want to make sure that you are not having problems with caching, you can remove the public directory, which is used by Hugo to build the blog.

$ rm -rf public && hugo server --navigateToChanged --buildDrafts --buildFuture --watch --verbose

Creating a new page

If you create a new section (e.g. faq), you will have to create a directory with a _index.md file. See existing directories like ./content/blog/ or ./content/tutorials/ for example.

To add a page to an existing section, the simplest option is to just copy an existing page. You can also create an empty Markdown page (e.g. ./content/faq/new-file.md).

If you are building the site with --watch, you should be able to navigate to that page already at http://localhost:1313/faq/new-file.html.

Existing pages (and posts) contain a YAML header, called “front matter”. You can copy an existing header as example.

---
title: Give it some nice title
---

This is markdown.

<p>Or HTML...</p>

Creating a new post

Blog posts are created in the directory /content/blog/. The existing posts were migrated from Jekyll, so we need to follow the existing pattern for consistency.

• 2020-01-20-url-friendly-title.md

In the example above, 2020-01-20 is the post date. This is not really used, but it can be added just for the sake of keeping up with the existing pattern.

The url-friendly-title is the part that will be used in the URL, so choose one that is unique and simple, with dashes or underscores.

Before writing the post content, the front matter YAML header needs to be added, as in the example below.

---
title: "Advanced Cross-Project Linking of Jenkins Artifacts"
description: "Linking Data-Source Builds and their Metadata"
tags: [Jenkins, workflow, data-sciences, analysis, bioinformatics, metadata]
author: Ioannis K. Moutsatsos
date: 2020-02-02
---

Any markdown **content** here. Like in GitHub.

<p>Or some <strong>HTML</strong>.</p>

The front matter header above defines a title, that appears in the web page generated. The description is used in the blog listing as a summary for the post (when visiting the URL /blog/).

The tags are used to classify the post. Fill in the author name and the date. The date will be used to produce the URL slug name (/2020/02/02/advanced... in the example above).

Preview your post locally — building and serving locally, as per instructions above — and commit to a pull request or to a branch like master once you are done. In a few seconds the GitHub Actions pipeline will run, and if it succeeds the site will be updated with your post.

GitHub Actions builds take seconds to one or minutes.

Contributing

All contributions are welcome! Send us your issues, pull requests or suggestions.

License

MIT

biouno.github.io's Issues

Create documentation to run mrbayes and figtree

http://www.biouno.org/tools/creating-a-pipeline-using-mrbayes%20and-figtree

Update Bruno's personal information on team page

Favicon

@imoutsatsos take a look at the new favicon. I used the old one first (the one that said Bio1), but it looked too small...

So tried B1... which is also a vitamin import for humans... life-sciences.... dad-joke level-up!!!

Anyway, here's the preview.

WDYT? Feel free to close the issue if it's good enough!

Add link on contact to add IRC web chat client on #biouno @FreeNode

Markdown Headers and Jekyll update

@kinow Saw your site via ropensci-archive/reproducibility-guide#89

One thing I noticed is that your markdown headers didn't have spaces between the # and the text. That was another thing that broke with the Jekyll update. It needs a space to render as a header. Caused me quite the headache on multiple sites!

Add a way to cite plug-ins

We could provide a screen or button that would provide the necessary information to cite the plug-ins and BioUno

Create documentation to run structure in parallel

http://www.biouno.org/tools/running-structure-in-parallel-with-jenkins

A must before sending a note to the mailing list

Create documentation to run mrbayes with biouno

http://www.biouno.org/tools/running-mrbayes-with-jenkins

Page Links for all tutorials are broken

For example link in this tutorial generate 404 (file not found errors)
http://biouno.org/tutorials/integrating-jenkins-rscript.html

Update website layout

This has been a topic in several of our hangouts. @imoutsatsos and myself discussed it and chose a couple of options (minimal-mistakes jekyll theme, and Groovy project web site).

I will start with minimal-mistakes, as our current site is using Jekyll, so it will be easier :-)

Fix link out of standard

http://www.biouno.org/tools/creating-a-pipeline-using-mrbayes%20and-figtree

Add BioDevOps and BioDocker to project links

Add under references, further reading, project links or some other similar section these two awesome projects:

• http://biodocker.github.io/
• http://biodevops.org/

Learned about these tools from this great post https://medium.com/@gawbul/devops-and-reproducible-science-628ffc839de3 by Steve Moss

Prefer HTTPS

Our site allows HTTP or HTTPS. It shouldn't matter much, but it would be nicer I think to give users HTTPS by default if possible for privacy. I also think SEO were giving preference to sites with HTTPS over HTTP.

Link to Blog Archive broken

http://biouno.org/archive.html link at the bottom of the
http://biouno.org/blog/ page is broken

Add documentation to create image galleries

http://www.biouno.org/tools/creating-graphs-with-r-and-creating-image-galleries

Add link to send publication

Add a send us your publication link

Add side bar to the landing page

Otherwise it's hard to understand what the site offers.

JModelTest2 integration

@rocherbpb suggested that we try integrating JModelTest2 to BioUno too.

Here's the link: https://code.google.com/p/jmodeltest2/

Add a tutorials section in the side menu

Use remote theme

Seeing

Your site is having problems building: A file was included in _pages/archive.md that is a symlink or does not exist in your _includes directory. For more information, see https://help.github.com/en/articles/page-build-failed-file-is-a-symlink.

After pushing the latest changes. Funny that it worked on my repository kinow.github.io. From the docs of the theme, they say

100% compatible with GitHub Pages when used as a remote theme.

So let's try to use it as a remote theme.

Image displayed when sharing links from biouno.org

Follow-up from #27

@imoutsatsos, should we have one image used for all links, or should we specify one per page? Google/YouTube/Twitter/FaceBook/etc try to get one image from the link shared.

But it also looks for Open Graph tags. They are special tags used in the HTML code to tell the other sites which information we have (it's some vocabulary from semantic web, you probably use something similar for metadata).

We can test it with a tool like this one: https://opengraphcheck.com/

Here's a post from NIWA: https://opengraphcheck.com/result.php?url=https%3A%2F%2Fniwa.co.nz%2Fnews%2Finternational-climate-experts-gather-in-wellington

And here's our main page: https://opengraphcheck.com/result.php?url=http%3A%2F%2Fbiouno.org%2F

So we have a few options:

• Add an image to landing page, with the open graph tags.
• When a post has an image, we have to remember to copy the example HTML with Open Graph annotations (or we can look for a Jekyll plugin that does that)
• Add a general image for Open Graph. But that way I don't believe we would be able to overwrite it. So it would be always the same image.

WDYT?

Move to Hugo

I've had issues with Jekyll and Ruby on Ubuntu LTS over past years (several times), but never had with Hugo in Apache sites and on my personal site.

@imoutsatsos also had issues with Ruby on Windows, so let's move the site to Hugo, and also add archetypes for the blog post, so that we can document the commands used to create a blog post, and the process to deploy a draft or final article, and how to run everything locally (and faster) with Hugo.

Image links for all tutorial are broken

While viewing tutorials on BioUno all image links seem to be broken

Update contact information

Update now that we have a biouno repository

Add image that hides video.

Once the user clicks on the image, the video is ajax-loaded. This way, users behind proxies won't see an error message.

Only cosmetics.

Update links/references

e.g. include

• BioUno
  • Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)
• PBS Plugin
  • Use of Continuous Integration Tools for Application Performance Monitoring
  • Continuous integration in a Cray multiuser environment
• R Plug-in
  • Jenkins Continuous Integration Cookbook - Second Edition
• Image Gallery Plug-in
  • A real example of how to implement Agile Testing

Add documentation to reproduce pipelines

http://www.biouno.org/docs/reproducing-an-existing-pipeline

Add roadmap

We must formalize the project roadmap in the web site.

Update license header

Include 2013

Write a ISA-TAB parser for Java

Interesting format for metadata. Looks like it's missing a Java implementation http://isatab.sourceforge.net/tools.html#filter-items

TODO: look for other parsers wild on the Web

Create update site

Create structure plugin documentation

That's a plug-in that needs more documentation. Once we have the docs, we need to drop a message at the structure mailing list.