Add Tool Shed integration

Hi Fidel,

the following commits, will add basic Tool Shed integration. UCSC Tools, deepTools, numpy, scipy, matplotlib and samtools will be automatically installed. computeMatrix and heatmapper is tested. I also cleaned up the code a little bit and fixed a few bugs in the wrappers.

The -p options is not implemented yet, because we are discussion right now how to do it 'in the right way' for the entire Galaxy suite. So that an administrator can specify a reasonable setting in the universe_wsgi.xml file or in the jobs_conf.xml file.

Have a nice weekend,
Bjoern