The following has a bit of advice on that:

http://www.admon.org/difference-between-login-shell-and-non-login-shell/

chris

On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote:

> How do I set my path in a non login shell?
>  
> From: George Marselis [mailto:george.marse...@kaust.edu.sa] 
> Sent: Tuesday, August 30, 2011 9:40 AM
> To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Tools requiring java can't find java
>  
> Yes, your java path is not set, because you are using an non-login shell. 
> Indeed, you should be talking to your sysadmins. 
>  
> ----
> George Marselis, systems administrator
> Building #2, Level 4, room 4327
> Computational Bioscience Research Center, KAUST
> Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
>  
> From: "Chorny, Ilya" <icho...@illumina.com>
> Date: Tue, 30 Aug 2011 19:23:42 +0300
> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> Subject: [galaxy-dev] Tools requiring java can't find java
>  
> This is probably a question for our sys admin but when I  run tools such as 
> GATK I get an error java command not found. I can execute java from the 
> command line and it works. Further I can grab the drmaa submission script (ie 
> galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any 
> thoughts?
>  
> Thanks,
>  
> Ilya
>  
>  
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com
> Website: www.illumina.com
>  
>  
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