Hey Michel, the NGS mapping tools (and others) consume significant computational resources and will have to wait on the line to be executed because there are separate nodes reserved for them. So, 2 days is normal in my own experience.
One thing you can do is to click on the option "Job Resource Parameters" which is located at the end of the form (in Bowtie, Bowtie2, Lastz...). Then change it to "Specify Job Resource Parameters", and after the page refreshes you just change from "Galaxy cluster (default)" to the "TACC Stampede test/development (beta)" and run the job again. I just did this running the same job both on the Galaxy cluster and on Stampede and the later finishes significantly faster. This is because the Stampede cluster is more powerful so, give it a try. o/