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:


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.





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