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<mailto:icho...@illumina.com>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>


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