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" 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>"
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>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/