Obviously the program fastx_clipper has not been found. It either has not been installed or is not in the PATH environment so the OS cannot find it

I will revise the install of Galaxy, or outside Galaxy, will make sure that the fastx-toolkit commands can be found, like copying the commands in a place defined in the PATH

If you are root run

echo $PATH

And look if a directory like /usr/local/bin is included

Then copy with a sudo cp order all of the fastx-tollkit commands there

If you are not root, ask for assistance

This is better suited to the Galaxy site, however since I run a couple Galaxy instances too perhaps I can help.

The fastx_clipper executable should be somewhere under /home/user/Downloads/galaxy-master/tool-deps (or something along those lines). You can check the exact place it's looking for it by looking in the shell script that you mentioned. For each job, the $PATH is modified in that script by sourcing various env.sh scripts. Those, in turn, contain the exact expected location of the executables.

Having said that, you could also remove and reinstall fastxtools from the toolshed, since that'll probably also fix the problem.