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 http://www.gnu.org/software/bash/manual/bashref.html#Bash-Startup-Files 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