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,****

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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?****

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Here is the wiki page: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies****

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Here is the section I am hoping will help:****

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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 fileshttp://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.****

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Thanks!****

Ryan****

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