make stops with error on building bowtie, etc, etc

[vlad-belogrudov]

make cannot proceed due to problems with downloaded archives - wget gets them in form archive.tar.gz.download but the script tries to unpack archive.tar.gz

The makefile also needs some cleanup to build only what is necessary - now it tries linux, mac, .. failing in the middle.

The doc mentioned everything for linux comes within a zip but it is not true anylonger

Best regards, Vlad