Thanks Nate! Updated documentation is always welcome and useful. I
appreciate the clarifications.


On Mon, Dec 12, 2011 at 10:18 AM, Nate Coraor <> wrote:

> On Dec 9, 2011, at 4:34 PM, Josh Nielsen wrote:
> > Hello,
> >
> > 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 (
> 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/?
> Hi Josh,
> There are two ways to do this.  The simplest is to place the binaries into
> a directory on the Galaxy user's $PATH.  The second is via the tool
> dependency system, which I need to write up documentation for to put in the
> wiki, which I'll do this week.
> > 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
> Java JARs are a special case, and FastQC has a unique way of locating its
> jars, which is why it is expected to be found in that directory.  This
> needs to be documented.
> >
> > 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.
> The list of external dependencies by tool is maintained here:
> I'll update this page with links to the new documentation when I write it.
>  I should also add that work is under way to make it possible to
> automatically install these dependencies as needed.
> --nate
> >
> > Thanks,
> > Josh
> > ___________________________________________________________
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> >

Josh Nielsen
Systems Administrator
HudsonAlpha Institute for Biotechnology
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