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