Thanks Jeremy,

That does clear quite a few things up. I will probably take the route of
just adding the directories that contain the tool executables to my path.
And I guess I'll just pay attention to which tools are Java based and copy
the executables under the jars directory. Thanks for looking on the wiki
too. If you find (or create) a suitable wiki page sometime soon would you
be so kind as to post a link to it here, for myself and posterity? That
would be great. Thanks for your help!

P.S. Sorry for the 'double post'. I don't use mailing lists often.


On Sat, Dec 10, 2011 at 8:33 AM, Jeremy Goecks <>wrote:

> Josh,
> 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/", line 141,
> in assert os.path.isfile(opts.executable),' error - cannot
> find executable %s' % opts.executable AssertionError: error -
> cannot find executable 
> /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
> *
> The exception to the above is Java-based tools. For these tools, you'll
> need to use the ~/galaxy-dist/shared/jars directory. This is a limitation
> of Galaxy that will likely be addressed in the future.
> 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.
> I looked a bit but couldn't find it; I suspect it is out on the wiki
> somewhere, though clearly it needs to be easier to find.
> Good luck,
> J.

Josh Nielsen
Systems Administrator
HudsonAlpha Institute for Biotechnology
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