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. : 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**** > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/