I have a question which I have not seen specifically addressed in the
online Galaxy wiki documentation about how to integrate tools
(dependencies) into Galaxy. I have implemented a locally managed instance
of Galaxy that my business is using with our cluster and now have a freshly
installed and configured instance of Galaxy running. It is bare-bones right
now and I did not use mercurial to sync any existing files/directory
structures. I have seen the page on external tool dependencies (
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) needed for
Galaxy, but I am somewhat unsure where to place the tools to utilize them
as intended (other than through trial & error).

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/?

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

To fix this I downloaded the FastQC tar file from its webpage, unzipped it,
and copied the fastqc binary/script to the "home/galaxy/galaxy
-dist/tool-data/shared/jars/FastQC/*"* directory. I also had to mkdir
FastQC/ under jars/ to place it there since it didn't already exist. Had I
not been told the specific directory by the error I'm not sure how I would
have intuitively known to place the binary there (unless I'm overlooking
some critical documentation). And how do I know that other similar things
are not missing which should be there? Can anyone shed some light on this
please? Adding a brief page on the Galaxy wiki site under the Admin section
about this would really help, even if it only showed an example for one or
two specific tools.

Josh Nielsen
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