Tab to spaces in XML file
Fix typo and reference to BLAST
Use MIRA 4.0 RC5 instead of RC4
Use new MIRA4 -t option to set number of threads
Attempt to auto-install MIRA4 under 64bit Mac OS X
Update installation & docs to target MIRA 4.0 (was using RC5)
Correct error handling when missing environment variable
Set MIRA4 environment variable during install (do we need PATH too?)
Install MIRA 4.0 under TravisCI
Use -NW:cmrnl=no with MIRA 4.0
Setting MIRA's number of threads via -t switch
Update copyright year
MIRA 4.0 manual now standardised on segment_placement etc with underscore
Cope with change to MIRA4 segment_placement for unpaired reads
Update sample E. coli assembly output for MIRA 4.0 (final)
Try two of the MIRA4 de novo tests under TravisCI
TravisCI seems to have too old a version of samtools for MIRA4
If provide all reference output files tests works

This is a workaround for a bug/design limitation in the Twill
based Galaxy test framework, otherwise due to a list-based
data structure the wrong files are compared to each other.
The new Galaxy API based test framework avoids this problem.

NOTE: Sample output files deliberately not checked in (~1MB).
Hack to avoid Twill test framework bug with omitted outputs
More verbose error message when missing MIRA4 binaries