On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics bioinformatics.umd@gmail.com wrote:
On Oct 14, 2013, at 9:16 PM, Brad Chapman chapmanb@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