Initial commit of scripts for setting up NeCTAR Cloud NGS Workshop.
Info on how to setup NGSWorkshop VM with data

Updated readme with details of how to setup a NGSworkshop VM on the
NeCTAR Research Cloud VM with the data required for the BPA NGS
workshop.
Formatting updates
Additional formmatting changes
!st major refactoring involving converting the NGS workshop docs into
LaTeX. Using Eclipse and TeXLipse for managing the project.
Changed protocol to https for swift object storage

NeCTAR recently changed from http to https.
get setup script from github

Get setup script from github instead of NeCTAR cloud storage.
Updated remaining urls

Updated urls to use github or https for swift object storage on the NeCTAR research cloud.
Major revisions!
Merge remote-tracking branch 'origin/master'
Using default mdframe and corrected bonus icon size.
Loads more changes to the styling but minimal to the RNA-Seq tutorial.
Loads more changes, including:
 1) Added QC module.
 2) Added "The Trainers" page
 3) Updated the listings environment for safe copy-paste and
    nice printable characters.
 4) Listing line numbers are no longer copied to the clipboard
    in Acrobat Reader - this is not the case for all PDF viewers
Moved module files into their own subdirectory.
Added \mailto to the email addresses on the module chapter pages.
Updated Paula's details
Lots more changes:
  1) Default paragraph separation in questions environment is 2cm. Thus
providing a default amount of space for the trainee to write answers.
  2) Use position "H" for tables and figures. i.e. force them to be
placed exactly where the module author wants them, rather than floating
them around for a better "fit"
  3) Added the Velvet de novo assembly module
  4) listings automatically add the backslash continuation character (\)
whenever lines are auto-broken onto multiple lines. These are also
nicely copy-and-pastable.
  3) Some slight formatting changes
Added environment in which answers to posed questions are excluded from
the PDF by default. Simply generate the "trainer's manual" by
uncommenting the %\settoggle{trainermanual}{true} line. The
trainer's manual has different page styling and the answers to questions
show up in the resulting PDF.

Also removed background shading from the bonus and advanced sections
since too much nesting of such environments looks like someone vomitted
over the PDF!
Update handout.tex

Remove "\vspace{-3em}" in "advanced" session to display the picture of bonus properly.
	new file:   alignment/alignment.tex
	new file:   chip-seq/chip-seq.tex