Ryan,

On our HPC setup, we use the modules system but its the same issue you are
running into.

A number of methods exists for setting up the correct path, for you, I
believe the easiest would be one of the two:


1) In your init script: source (or setup) PATHS as you have them in your
.bash_profile.
    /etc/init.d/galaxy

OR

2) Within Galaxy, edit universe_wsgi.ini and look for:
    environment_setup_file
and create a file that will setup the correct $PATH for you.


You can also invoke the Tool Dependency options for each specific tool you
load as shown in[1].

[1]: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Wed, Sep 11, 2013 at 10:18 AM, Ryan Davis <rrda...@ucdavis.edu> wrote:

> Hi,****
>
> ** **
>
> We have a local server running Galaxy and a majority of the tools work
> correctly (bowtie, BWA, samtools and etc…).  I am having issues with some
> of the FASTX-Toolkit tools.  I am starting Galaxy with an init script on
> Centos 6 and the tools are in my $PATH and work at the command line, just
> not in Galaxy.  The wiki suggest to “set $PATH in the startup file or
> use.” ****
>
> It leaves me hanging and don’t know what the other option is.  Can someone
> share with me their workaround?****
>
> ** **
>
> Here is the wiki page:
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies****
>
> ** **
>
> Here is the section I am hoping will help:****
>
> ** **
> Local Jobs****
>
> Changes to $PATH can be persisted by setting them in your shell's startup
> file(s).  This typically means ~/.bash_profile for bash, but please see
> the bash documentation on startup 
> files<http://www.gnu.org/software/bash/manual/bashref.html#Bash-Startup-Files>
>  or the *INVOCATION* section of the bash(1) man page to understand the
> intricacies of how that file is read.  Of particular importance, if you are
> starting Galaxy in a method other than manual invocation from a shell
> prompt (with sh run.sh) such as with an init script, it is likely that
> your startup file will not be read.  In this instance, you should set
> $PATH in the startup file or use.****
>
> ** **
>
> ** **
>
> Thanks!****
>
> Ryan****
>
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