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.commailto:ichorny@illumina.com> Date: Tue, 30 Aug 2011 19:23:42 +0300 To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto: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.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com

Gah, wrong link, apologies (the other one is okay, if a bit wonky):

http://www.linuxfromscratch.org/blfs/view/cvs/postlfs/profile.html

chrus

On Aug 30, 2011, at 1:12 PM, Chris Fields wrote:

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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