On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics
<bioinformatics....@gmail.com> wrote:
> 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.
>

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
___________________________________________________________
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/

Reply via email to