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

[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" 
>> Date: Tue, 30 Aug 2011 19:23:42 +0300
>> To: "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
>> 
>> 
>> ___
>> Please keep all replies on the list by using "reply all"
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>> and other Galaxy lists, please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 


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

[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" 
> Date: Tue, 30 Aug 2011 19:23:42 +0300
> To: "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
>  
>  
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


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

[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" mailto:icho...@illumina.com>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
mailto: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<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>


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

[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" mailto:icho...@illumina.com>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "galaxy-dev@lists.bx.psu.edu" 
mailto: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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