Hi Jeff,

On Apr 28, 2011, at 12:42 AM, Whyte, Jeffrey wrote:

> Hi Pieter,
> 
> Thanks to both you and Florent for the suggestion of MacPorts.  GnuPlot is 
> now working well in Galaxy after I installed the port.

:)

>  I also appreciate the information on specifying the custom environment.  
> That could be related to the only other problem I am having: the FASTX 
> toolkit barcode splitter.  Other FASTX tools like "rename sequences" and 
> "trim end" work just fine, but the barcode splitter gives the following error 
> in Galaxy:
> 
> An error occurred running this job:sed: illegal option -- r
> usage: sed script [-Ealn] [-i extension] [file ...]
> 
> Unfortunately, I don't believe there is a port of the FASTX tools available 
> through MacPorts.  I have gone through the instructions on the Hannon Lab 
> webpage to try to install exactly as specified, but still get the error, 
> although now at least Galaxy knows where to look to find the tools.  I don't 
> believe this is related to the PATH, as the error in Galaxy seems to relate 
> to an option setting.

That seems correct. I just checked sed on a Mac OS X laptop and a linux server: 
the one distributed with Mac OS X does not have a --r option whereas the one on 
Linux does. 

>From man sed on linux:

  -r, --regexp-extended
                 use extended regular expressions in the script.

There is no -r in sed on Mac OS X, but from man sed:

     -E      Interpret regular expressions as extended (modern) regular 
expressions rather than basic regular expressions (BRE's).  The
             re_format(7) manual page fully describes both formats.

Just from the description this -E option seems extremely similar if it isn't 
just plain the same, so you may try to change the sed -r command into sed -E in

        galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh

If that doesn't work you either have to hack the code of this tool :o or try to 
install a compatible version of sed...

Cheers,

Pi

> I have run this barcode splitting on the public Galaxy server with no 
> problems, and I simply used the same barcode definitions and joined file in 
> my local instance of Galaxy, but get the error.
> 
> I'll give you a break :) and keep working on it to see if I can trace the 
> source of the error.
> 
> Many thanks again,
> Jeff
> 
> 
> On Apr 27, 2011, at 4:10 AM, Pieter Neerincx wrote:
> 
>> Hi Jeff,
>> 
>> 1. As Florent wrote, probably the easiest solution is to install the 
>> dependencies with MacPorts. Only if stuff is not available via MacPorts or 
>> the version available is too old / incompatible with other dependencies I 
>> install things manually. MacPorts will add a line like this:
>> -----------------------------
>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH 
>> -----------------------------
>> to your ~/.profile file, which is automatically sourced when you open a new 
>> Terminal window. Galaxy is probably running using a different account than 
>> yours. Usually a dedicated one or one used for the webserver like _www or 
>> www or apache or ... This user must have the same addition to it's 
>> environment in order to find gnuplot et al. To give Galaxy the same 
>> environment you can either add the line above to galaxy/run.sh immediately 
>> after the first line that identifies the file as a shell script (#!/bin/sh) 
>> and before the code that starts Galaxy. Optionally you may specify the 
>> environment in a separate file and source this file. Personally I like the 
>> latter, because I can manage the environment for multiple users and software 
>> packages in a single file that I can call from various locations. To source 
>> a file you use the . command. Hence [dot][space][path to env file]. Your 
>> galaxy/run.sh would start like this:
>> -----------------------------
>> #!/bin/sh
>> 
>> #
>> # Source my custom environment including the path to MacPorts and other 
>> stuff I installed outside the default search paths
>> #
>> . /path/to/our_environment.bashrc
>> -----------------------------
>> 
>> In our_environment.bashrc you would than have the same line:
>> 
>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH
>> 
>> and potentially other stuff to set your environment. 
>> 
>> 2. For the gnuplot error below "unknown or ambiguous terminal type": It 
>> seems the gnuplot script Galaxy is calling is trying to use an unsupported 
>> "terminal". When you save the figure to a file a "terminal" is just a file 
>> type. In order to write jpeg, tiff, png, pdf, svg, etc. images gnuplot uses 
>> several libraries. When you install gnuplot it will look which libraries are 
>> available and based on that some image file formats may be available and 
>> others will not. It seems png support is not available. When you start a 
>> gnuplot terminal and type 'set terminal' for a list, do you see png as a 
>> supported terminal? If not, you should probably install libpng first and 
>> re-compile gnuplot. If you install gnuplot via MacPorts though it will 
>> probably already take care of this dependency and install it for you... 
>> 
>> Cheers,
>> 
>> Pi
>> 
>> 
>> On Apr 24, 2011, at 3:57 AM, Whyte, Jeffrey wrote:
>> 
>>> Hi Pieter,
>>> 
>>> Thanks very much for taking the time to provide the advice and explanations 
>>> - very helpful!  As you suggested, my search path was not defined properly 
>>> to locate gnuplot.  If I typed "gnuplot" in the Terminal, I would get the 
>>> message, "command not found".  Now, Gnuplot is in /usr/local/bin and this 
>>> directory is listed when I type "echo $PATH".  Now when I type "gnuplot" in 
>>> the terminal, I get:
>>> 
>>> $ gnuplot
>>> 
>>> G N U P L O T
>>> Version 4.4 patchlevel 3
>>> last modified March 2011
>>> System: Darwin 10.7.0
>>> 
>>> Copyright (C) 1986-1993, 1998, 2004, 2007-2010
>>> Thomas Williams, Colin Kelley and many others
>>> 
>>> gnuplot home:     http://www.gnuplot.info
>>> faq, bugs, etc:   type "help seeking-assistance"
>>> immediate help:   type "help"
>>> plot window:      hit 'h'
>>> 
>>> Terminal type set to 'aqua'
>>> gnuplot>
>>> 
>>> When I start up Galaxy, and try to run the Boxplot tool, I now get a 
>>> different error:
>>> 
>>> An error occurred running this job:
>>> gnuplot> set term png size 2048,768
>>> ^
>>> line 0: unknown or ambiguous terminal type; type just 'set terminal' for a 
>>> list
>>> 
>>> gnuplot> plot '/Users/JJWhyte/galaxy-dist/database/files/000/dataset_6.dat' 
>>> using 1:7:11:12:9 with candlest
>>> 
>>> I think this is related to the environment, as you explained in your second 
>>> paragraph.  I tried starting gnuplot from the Terminal first, then typing 
>>> "set term xterm", and then exiting, but this didn't change the error.  
>>> Could you please explain how you set the environment in the galaxy/run.sh 
>>> script?
>>> 
>>> Again, I appreciate the help.
>>> 
>>> Jeff
>>> 
>>> 
>>> 
>>> On Apr 23, 2011, at 8:11 AM, Pieter Neerincx wrote:
>>> 
>>> Hi Jeff,
>>> 
>>> 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:
>>> 
>>> echo $PATH
>>> 
>>> 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.
>>> 
>>> Cheers,
>>> 
>>> Pi
>>> 
>>> 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 
>>> 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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>>> 
>>> 
>> 
>> -------------------------------------------------------------
>> mobile: +31 6 143 66 783
>> e-mail: pieter.neeri...@gmail.com
>> skype:  pieter.online
>> -------------------------------------------------------------
>> 
> 

-------------------------------------------------------------
mobile: +31 6 143 66 783
e-mail: pieter.neeri...@gmail.com
skype:  pieter.online
-------------------------------------------------------------


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