I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin

And I've set the PATH environment in the galaxy user's .bashrc

export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"

When I  echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node

/mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin

But I always see /bin/sh: bowtie: not found