delly 0.3.3

Add option to install 64-bit binary on Linux.

Closes #813.
R 3.1.0

R 3.1.0 (codename "Spring Dance") was released April 10, 2014.

More information at:
https://stat.ethz.ch/pipermail/r-announce/2014/000572.html

Closes #815.
Closes #821.
bedops 2.4.2

Closes #820.
bowtie 1.0.1
graph-tool 2.2.31

Closes #802.
insighttoolkit 4.5.2

Closes #824.
bowtie2 2.2.2
octave 3.8.1: optional GUI & JIT
Fix for odd mkoctfile dependency issues
X11/TeX fixes
EXPERIMENT: stripping out extra link dependencies in mkoctfile, to see if it fixes the pkg problems.
Removed the keyboard patch for HEAD builds; added mkoctfile patch, pstoedit/epstool dependencies
Further remove unnecessary link dependencies in mkoctfile.
Added X11 lib path fix back in
Moved the X11 replacement to the proper place