Fix typo in ipython config file template
Add AlienTrimmer and featureCounts to minimal flavor.
Workaround for bowtie 2.2.0 not working with Tophat.

'Note: the latest version of Bowtie2 (v2.2.0) is not compatible with TopHat2.
We will fix this issue soon.'

So for now go back to installing from source so we can use the 2.1.0 version
which works.
Add bowtie2 back into the custom installer.

Previous commit just disabled homebrew installation of bowtie2.