> 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)?

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