I am having an issue with some of the tools in my local galaxy. I can download and run some tools (Bowtie2), yet others do not work (MACS2). I looked at where the tools are being downloaded, and am questioning if the location is correct. Instead of going to my 'drive'/galaxy path, they are going to the 'drive'.
Do they need to be in the galaxy folder? If so, where in the galaxy.ini file do I make this change? Or, is it that the tools need to be reinstalled?