It appears that there are shell directories for the tools under ~/galaxy-dist/tools/ with basic wrapper scripts but without the corresponding executables (very few that I've noticed have the tools already in them). Is the intent to download the dependency tools and (building from source if necessary) take the binaries in those directories and copy them to their corresponding directory under ~/galaxy-dist/tools/? This seems to have worked with an error I first got when clipping a FASTQ file which reported that fastx_clipper was not a recognized command. So I downloaded the FASTX Toolkit, compiled the binaries, and copied only the binaries into the corresponding fastx tools directory. Would I do the same thing for TopHat and Cufflinks by taking all their binaries (combined) and copying them into ~/galaxy-dist/tools/ngs_rna/?
You'll want to read about Galaxy Tool files a bit to understand the files in ~/galaxy-dist/tools:
These are not shell directories; instead, they include tool config files + additional wrapper scripts to run a tool in Galaxy.
To answer your question, executables for tools need to be in your path but do not need to be in the config/wrapper directories. For example, in an SGE cluster, we suggest setting the PATH environment var in ~/.sge_request
Even if that is the case though, I have occasionally gotten errors about tools missing in completely different directories. One was for the FASTQ Groomer. One user saw this error in their browser (which for now is the only way I know to figure out where tools are *expected* to be):
File "/home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 141, in
assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc