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:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#Admin.2BAC8-Tools.2BAC8-Tool_Config_Syntax.Galaxy_Tool_XML_File

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.

Good luck,
J.


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