Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread George Marselis
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 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 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: icho...@illumina.commailto:icho...@illumina.com
Website: www.illumina.comhttp://www.illumina.com


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Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chorny, Ilya
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 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 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 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: icho...@illumina.commailto:icho...@illumina.com
Website: www.illumina.comhttp://www.illumina.com


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Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chris Fields
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.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 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 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 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
 Website: www.illumina.com
  
  
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Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chris Fields
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.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 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 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 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
 Website: www.illumina.com
 
 
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 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
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 http://lists.bx.psu.edu/
 


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