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)? Brad ___________________________________________________________ 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/
