Thank you very much. What I ended up doing to fix this issue was to uninstall 
fastx_toolkit from the tool shed then I created a .bashrc file for galaxy. I 
added this to the environmental_setup_file path and restarted galaxy. This was 
the fix I needed. Things seem to be working now. Here is the contents of my 
.bashrc file for others having issues.

export PATH=${PATH}:/usr/bin:/usr/local/bin:/bin:/opt/local/bin:/opt/local/sbin

I placed the .bashrc file in the galaxy-dist folder and source it from there. 


On Oct 15, 2013, at 9:53 AM, Carlos Borroto <> wrote:

> On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics
> <> wrote:
>> On Oct 14, 2013, at 9:16 PM, Brad Chapman <> wrote:
>>> Ian;
>>>> I have my PATH set as well as the and my ./bash_profile. Again
>>>> this all works fine from the command line. I don't know where else
>>>> Galaxy is trying to find the fastx commands.
>>> I know zero about setting up fastx_toolkit from the toolshed but from
>>> reading your error messages:
>>>> command not found cat: stdout: Broken pipe
>>>> command not found gzip: stdout: Broken pipe/
>>> It looks like it's not having trouble finding fastx_toolkit, but rather
>>> standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
>>> feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
>>> wherever cat and gzip are on your system)?
>> This is what I have for cat and gzip
>> $ which cat
>> /bin/cat
>> $ which gzip
>> /usr/bin/gzip
>> $ echo $PATH
>> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:
>>> From what i can tell they should be available on the $PATH so I'm not quite 
>>> sure why Galaxy cannot "see" them.
> Hi Ian,
> In the past I had trouble making sure Galaxy would run jobs with the
> proper environment settings. I think there are a few moving parts
> depending on your local configuration(ex. local vs cluster jobs). All
> of my problems went away after I started using something like this in
> my 'universe_wsgi.ini':
> environment_setup_file = /local/opt/galaxy/.bashrc
> Any env configuration I want Galaxy to use, I put it in that bashrc file.
> Hope it helps,
> Carlos

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