Ritchie Lab website

Source of the Ritchie Lab website (Jekyll, served by GitHub Pages). Pages: About (index.markdown), Software (software.markdown), Datasets (datasets.markdown).

The Software and Datasets pages are generated from one small file per entry, so you never edit the page layout to add something: you add a file (and an image) and commit.

Add a software package

1. Add the icon. Put a square PNG (about 200x200 px or larger) in assets/images/software/, e.g. assets/images/software/mytool.png.

2. Add the entry. Create _software/mytool.markdown (any file name, .markdown):

   ---
   name: MyTool
   github: https://github.com/mritchielab/MyTool
   bioconductor: https://bioconductor.org/packages/release/bioc/html/MyTool.html
   papers:
       -
           name: Title of the paper
           url: https://doi.org/10.xxxx/xxxxx
       -
           name: Title of a second paper
           url: https://www.biorxiv.org/content/10.1101/xxxx
   icon: mytool.png
   description: One-sentence description of what the software does
   ---

   • name, github, icon and description are needed.
   • bioconductor and papers are optional: delete those lines if not applicable (the Bioconductor button and the Publications list then do not appear).
   • icon is the file name inside assets/images/software/.

3. Commit and push. The package appears on the Software page and in the icon index at the top of it.

Add a dataset

1. Add the figure. Put an image (PNG, JPEG or WebP; a landscape figure works best) in assets/images/datasets/, e.g. assets/images/datasets/mydata.png.

2. Add the entry. Create _datasets/mydata.markdown:

   ---
   name: MyData
   datasets:
       -
           name: GSE000000
           url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE000000
       -
           name: Second accession
           url: https://example.org/second-dataset
   code: https://github.com/mritchielab/MyData_workflow
   papers:
       -
           name: Title of the paper
           url: https://doi.org/10.xxxx/xxxxx
   icon: mydata.png
   ---

   • name and code (link to the analysis code) are needed.
   • datasets (data accessions), papers and icon are optional: delete the lines you do not need.
   • icon is the file name inside assets/images/datasets/.

3. Commit and push. The dataset appears on the Datasets page.

Notes

• Order: entries are listed alphabetically by file name. To move an entry, rename its file.
• Colons in text: a colon followed by a space inside a value breaks the YAML. Either put the value in double quotes (name: "Glimma: interactive graphics") or write the colon as :.
• Indentation: use spaces (not tabs) and keep the - list items lined up as in the examples above.
• Preview locally (optional): bundle install then bundle exec jekyll serve, and open http://localhost:4000. The generated _site/ folder is git-ignored: do not commit it.
• Hosting under a sub-path: pages use relative links (see _includes/rootpath.html), so the site also works when served as a project page such as username.github.io/repo-name/.