14 Oct
2013
14 Oct
'13
8:16 p.m.
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