Running alinen assemblies
Updating the ray binary because kmer max size was not set
Moved gene clustering script to the 'scratch' repository
Sending new assembly jobs tests
Setting up GEFES on the cray
Added options to Ray object
First full test on the sisu machine
Adjusting to sisu limits
Update todo
Designing a more flexible format for the JSON files
Working on the mapper bowtie
Updating README
Updating README (bis)
Updating README (bis)
Added png versions
The branch that was 'master' is now called 'old'. The branch that was 'hackathon' is now the 'master' branch.

Merge branch 'master' into hackathon