The following has a bit of advice on that: http://www.admon.org/difference-between-login-shell-and-non-login-shell/ chris On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote:
How do I set my path in a non login shell?
From: George Marselis [mailto:George.MARSELIS@KAUST.EDU.SA] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java
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
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