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/
aebrenne@uci.edu


On Wed, Sep 11, 2013 at 10:18 AM, Ryan Davis <rrdavis@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 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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