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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