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" <ichorny@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: ichorny@illumina.com

Website: www.illumina.com