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
, Skype: project2501a
From: Chorny, Ilya icho...@illumina.commailto:icho...@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
How do I set my path in a non login shell?
From: George Marselis [mailto:george.marse...@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
, 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
Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
From: Chorny, Ilya icho...@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
