On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote: > I have the software for our SGE cluster (eg. Bowtie) in > /mnt/ngswork/galaxy/sw/bin > And I've set the PATH environment in the galaxy user's .bashrc > > export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH" > > When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job > runner node > > /mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin > But I always see > /bin/sh: bowtie: not found > > As an error message. > > > How can I get the path set correctly?
Hi Brad, I'd suggest putting it in ~/.sge_request rather than ~/.bashrc. This will ensure that running jobs differently (qsub vs. the DRMAA API) won't affect setting $PATH or other environment variables. See past discussions on the list for more on .sge_request: http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=815885&query=sge_request --nate > > > > > > > Brad > -- > Brad Langhorst > New England Biolabs > langho...@neb.com > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/