bowtie2 rewrite

Complete rewrite of bowtie2 wrapper to support almost all command line options as well as dataset collections
Is this really save? I'm really sceptical to give command line access to users in any way (if this is not in docker ;)).
For the `sed` or `awk` wrappers we implemented a special sandbox mode to it more secure. If the user really wants to use command line mode, he should use IPython or a special IE for this.