On Oct 14, 2013, at 9:16 PM, Brad Chapman <chapm...@50mail.com> wrote:

> 
> Ian;
> 
>> I have my PATH set as well as the env.sh 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. 

Ian

> 
> Brad


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