How do I set my path in a non login shell?

From: George Marselis []
Sent: Tuesday, August 30, 2011 9:40 AM
To: Chorny, Ilya;
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" <<>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "<>" 
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 and qsub it from the command line and it finds JAVA. Any 



Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582

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