Include 9 Dec 2014 date for upcoming course
Formal publication of Baggerly and Coombes arxiv preprint
Explicit path to data (setup in morning); tweak BLAST commands

Was missing call to script and duplicated next example.
Explicit line break (cosmetic)
Explicit line break (cosmetic)
BLAST commands from part 2
First step of the annotation workshop
Merge pull request #1 from peterjc/dec2014

Minor updates for Dec 2014 course; filling in exercises.tex
Commands for gene prediction and BLAST genome comparison
Adjust path to match folder structure we'll be using
Copy the MUMer commands to exercises.tex
Tweaks to fit commands on one page (two sides).

This reduces the page margins, supresses the vertical space left for
a caption on each code listing, and comments out the art and act
commands (since we will probably run those from the host Windows
machine rather than over X Windows remotely).
Use LaTeX listings option breakatwhitespace=true

There are still several annoyingly long commands which have to be
split over multiple lines, but this way the split happens on
spaces rather than for example after the hyphen in '-outfmt 6'
or after the dot in 'chrA_NC_0004547.filter' which is confusing.
Crude Makefile for the presentation PDF files.

Does not handle the child section/*.tex dependencies properly, so will tend
to rebuild everything.
Remove 'afternoon' in text; Ensure in right path for example.

Note that the first example using the data/ex2_blast folder is done
within a script call, so on exiting script the user returns to the
previously used directory.
Merge pull request #2 from peterjc/dec2014

Remaining tweaks used for workshop today