This is indeed a dependency issue and I have seen those both on Linux and Mac
OS X. What happens if you type gnuplot in a Terminal window yourself? If you
also get "command not found". There is either still something missing or your
environment is not setup properly. If the tool works if you execute it yourself
in the Terminal, but it fails in Galaxy, you do have all the dependencies and
it's clearly an environment setup issue: your OS will search for the binaries
in a search path defined by the $PATH environment variable. This means that if
you call "gnuplot" without specifying the path where it is installed, the OS
will look in all directories specified in $PATH to find it. If it cannot find
it, it will give you "command not found". Additionally you may have to set
$LD_LIBRARY_PATH as well if the installed tools link to libraries installed
outside "default" locations.
Hence if you go to the Terminal and type:
You will see a colon separated list of directories that should include the
location where the gnuplot binary is installed. If this is not the case, please
Google for setting $PATH on Mac OS X. If gnuplot does work if you execute it on
the commandline, but it fails in Galaxy, it most likely means the environment
for the user used to run Galaxy is different from yours (and the location where
gnuplot is installed is missing from $PATH). In that case you can either set
the environment in the galaxy/run.sh script used to start Galaxy or if you can
call a bashrc script to set the environment from galaxy/run.sh. I use the
latter where I have one bashrc script that sets the environment for all users
and by calling this one from galaxy/run.sh I make sure the environment for
Galaxy is exactly the same as for my (command line) users.
On Apr 22, 2011, at 5:25 PM, Whyte, Jeffrey wrote:
> Hi Everyone,
> I'm having trouble getting some of the tools to work on my local installation
> of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy
> wiki are clear, and I was able to download and install from the anonymous
> Mercurial repository. Galaxy starts up and runs just fine for tools like
> "Get Data", "FASTQ Groomer", and "FASTQ Summary Statistics".
> The problems started when I try to run Graph/Data Display -> Boxplot
> (GnuPlot). I get the error:
> "An error occurred running this job:/bin/sh: gnuplot: command not found
> Error running gnuplot."
> The FASTX Barcode Splitter also gives me an error:
> "An error occurred running this
> line 65: fastx_barcode_splitter.pl: command not found
> zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file
> or directory
> sed: illegal opt"
> I'm assuming these are Tool Dependency problems, although I have tried to
> install the OS X versions of GnuPlot and the FASTX Toolkit and still get
> Are there any suggestions from users who are successfully running Galaxy on
> OS X?
> Thanks in advance,
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: