BioReports

Jekyll template for shared report generation.

What is BioReports?

This is a Jekyll site framework meant to be used in conjunction with a Custom version of Jekyll and Hastie – a command line tool for quick report creation.

How to use?

Clone this repository to a location accessible by all people who need to make reports.

git clone [email protected]:vlandham/hastie.git /shared/drive/location/bioreports_source

Create a server branch of the BioReports repository

git branch server
git checkout server

Modify the .gitignore in the server branch to remove exclusions of _posts/ and data.

Modify _config.yml and _server_config.yml as you see fit.

Add more plugins or javascript or css.

Ensure you have the forked version of Jekyll accessible to all report creators.

which jekyll
# /shared/gems/custom/jekyll

Ensure you have Hastie accessible to all report creators.

Create .hastie files for all users to point to bioreports_source location.

hastie config /shared/drive/location/bioreports_source

Now when you use hastie publish it should publish to your bioreports_source directory which will in turn update your bioreports page.

Enjoy!

Also, see Hastie Readme for more information on the motivation of this project, as well as how to run Hastie.

BioReports Features

There are a number of tools built into BioReports that are useful to our setup. Your mileage may vary.

_plugins/

• liquid_table_block.rb
  • quickly convert tsv or csv content to an html table.
• liquid_all_links.rb
  • Provide paths to files on shared drives – no matter the OS.
• liquid_data_link.rb
  • Generate a separate table page for large files. Place button to find this file in the report.
• generic_index.rb
  • ripped off another site. Used to generate report lists for labs (categories).

js/

• d3
  • For future plans to automate visualizations
• bootstrap
  • version of twitter bootstrap – just in cases
• jquery 1.6.2
  • Everyone needs jquery – right?
• tablesorter
  • Make every table a fancy table
• picnet table
  • For large tables
• jquery tableofcontents
  • automate creation of TOC
• script.js
  • Add show / hide and other features automatically to report sections

css/

• reset.css
  • based on html5boilerplate style.css
• style.css
  • custom stylings for custom tables, images, etc.

layouts/

• report.html
  • Nice looking start for your reports

posts/

• some example posts to get you started