Jeff, I haven't tried GnuPlot specifically in Galaxy, but all the applications that you install with MacPorts are installed under /opt/local/bin. I think that MacPorts adds this folder to your $PATH. So yes, Galaxy should be capable of finding any program that you installed through MacPorts. Florent On 24/04/11 12:22, Whyte, Jeffrey wrote:
Hi Florent,
I installed MacPorts this afternoon, but that was after I installed gnuplot (sudo make install). Have you found that gnuplot works in Galaxy if installed through MacPorts? Thanks for the suggestion.
Jeff
On Apr 23, 2011, at 7:03 PM, Florent Angly wrote:
Hi Jeff Some of these tools can be installed easily on Mac OS using MacPorts port search gnuplot Of course, you have to install MacPorts first. Florent
On 23/04/11 01:25, 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 job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: 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 errors.
Are there any suggestions from users who are successfully running Galaxy on OS X?
Thanks in advance, Jeff
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