Or you could create a directory in tool-deps called bowtie under bowtie create 
a default directory and in default create an env.sh file which set yours path 
correctly. 



-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: Friday, December 02, 2011 7:42 AM
To: Langhorst, Brad
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] PATH env variable for SGE jobs

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:/us
> r/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
> 
> 
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