Pull jobTree
Merge branch 'master' of https://github.com/glennhickey/progressiveCactus
Warn about high repeat or N content in input genomes (fixes #14)

Initial setup will be slower.
biopython install didn't work when not in a tty
Fix tokyocabinet build on systems without zlib-dev
Pull hal to fix annoying hal2maf bug in automated testing
pull hal to fix halAlignability and rename it to halAlignmentDepth
merge development