On Feb 8, 2011, at 5:21 PM, Nate Coraor wrote:

John Powell (NIH/CIT) [E] wrote:

...

Trying to install a local copy of Galaxy for evaluation. Downloaded the "stable" version using:

hg clone https://bitbucket.org/galaxy/galaxy-dist

I am installing it on a Centos 5 x86_64 Linux kernel which has python 2.4.3 installed. When running "sh setup.sh" the installation stops with an error building the "python_daemon" egg. In checking, it is trying to download/build python_daemon 1.5.5 (specified in the eggs.ini). This version of python_daemon uses syntax that depends on python >= 2.5. Your "README" indicates....

Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run: ...

Does Galaxy still run under python 2.4?

John,

It should, and the fact that it doesn't is a bug. I should have a fix for this shortly.

--nate

Hi John and Nate,

But to make the tool search work in the web interface you'll need Python 2.5 or higher, so it's probably a better idea to get a newer version of Python anyway. (We have Galaxy on two CentOS servers, installed a newer Python in addition to the OS supplied Python 2.4 and modified the environment for Galaxy so it uses the newer version: was easy to do and works well.)

Cheers,

Pi

...

(PS: I have lots of Linux/Perl experience, but virtually no python expertise.)

Thanks....

//=\ John Powell, CAPT, Ret. USPHS Phone: (301) 496-2963 =// Building 12A, Room 2033 FAX: (301) 402-2867 //=\ National Institutes of Health =// Bethesda, MD 20892-5624 Work: jip@helix.nih.gov //=\ Personal: jpowell@erols.com =// //=\ BioInformatics & Molecular Analysis Section-BIMAS/CBEL/CIT/NIH

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Hi Pieter and Nate,

Thanks for the information. I am in the process of having python 2.5.5 installed under "/usr/local/BIMAS/python_255/" on our system. Pieter indicated it was "easy" to setup galaxy to use an alternate installation of python. Any tips on what needs to be changed/configured before setting things up (./setup.sh) and for subsequently running galaxy (./run.sh)?

Thanks again...

At 09:54 AM 2/9/2011, Nate Coraor wrote:

Pieter Neerincx wrote:

...

Hi John and Nate,

But to make the tool search work in the web interface you'll need

Python 2.5 or higher, so it's probably a better idea to get a newer version of Python anyway. (We have Galaxy on two CentOS servers, installed a newer Python in addition to the OS supplied Python 2.4 and modified the environment for Galaxy so it uses the newer version: was easy to do and works well.)

-------- //=\ John Powell, CAPT, Ret. USPHS Phone: (301) 496-2963 =// Building 12A, Room 2033 FAX: (301) 402-2867 //=\ National Institutes of Health =// Bethesda, MD 20892-5624 Work: jip@helix.nih.gov //=\ Personal: jpowell@erols.com =// //=\ BioInformatics & Molecular Analysis Section-BIMAS/CBEL/CIT/NIH -------------------------------------------------------------------------

Hi John,

Don't mean to chime in, just my two cents... if you are installing local Python for Galaxy instead of using the older rpm Python on CentOS might as well install Python 2.6.6 since it probably has more features and better performance (my educated guess), I use 2.6.6 for a long time on my installation on RHEL5 which is the same as CentOS and everything in Galaxy works perfectly

-Leandro

On Wed, Feb 9, 2011 at 11:52 AM, John Powell (NIH/CIT) [E] jip@helix.nih.gov wrote:

Hi Pieter and Nate,

Thanks for the information.  I am in the process of having python 2.5.5 installed under "/usr/local/BIMAS/python_255/" on our system.  Pieter indicated it was "easy" to setup galaxy to use an alternate installation of python.  Any tips on what needs to be changed/configured before setting things up (./setup.sh) and for subsequently running galaxy (./run.sh)?

Thanks again...

At 09:54 AM 2/9/2011, Nate Coraor wrote:

...

Pieter Neerincx wrote:

...

Hi John and Nate,

But to make the tool search work in the web interface you'll need Python 2.5 or higher, so it's probably a better idea to get a newer version of Python anyway. (We have Galaxy on two CentOS servers, installed a newer Python in addition to the OS supplied Python 2.4 and modified the environment for Galaxy so it uses the newer version: was easy to do and works well.)

--------  //=\    John Powell, CAPT, Ret.  USPHS Phone: (301) 496-2963  =//    Building 12A, Room 2033        FAX:   (301) 402-2867   //=\   National Institutes of Health   =//   Bethesda, MD 20892-5624        Work:     jip@helix.nih.gov    //=\                                 Personal: jpowell@erols.com    =//     //=\ BioInformatics & Molecular Analysis Section-BIMAS/CBEL/CIT/NIH  -------------------------------------------------------------------------

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