Updated QualiMap version
Cleanup setup script
Removing legacy files
Update a lot of instructions in README
Assuming Piper on path
Update usage messages.
Moving legacy code to legacy dir...

... this code will be removed in the future.
Correct usage of only alignment according ...

... to the new system for picking which steps in the analysis are to be run.
Merge pull request #5 from Smeds/devel

 RNACounts will now load samtools and bowtie2, which is needed to perform tophat alignment. Tophat version has also been updated.
Update Readme by jess
Update read me again
some more small ones
some other small ones
last changes
Merge pull request #6 from jessieno/devel

read me proof read by Jessica.
Do not expand PATH variable in setup message
Accidentally commented out and commited...

... download and compile of the GATK. Woops!
Bumping version to v1.2.0-beta1