> 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
You'll want to read about Galaxy Tool files a bit to understand the files in
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
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.
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