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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Another vote for the excellent modules system from us at AgResearch. I think it's the only sane way to manage PATH, etc, when you have multiple versions of tools installed. http://modules.sourceforge.net/ I know I've said this before here. Tell all your friends. ;-)

Galaxy's dependency injection works in a similar way, without requiring all the external dependencies. We don't need unload since we compose a unique environment for every tool execution. This is much cleaner that loading everything into the environment before running Galaxy, we want tools to be executed with as clean an environment as possible.