Installation Issue on Centos/python 2.4
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? (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 -------------------------------------------------------------------------
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
(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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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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------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online -------------------------------------------------------------
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.)
This is correct, some optional features now require Python 2.5 or higher, and overall support for Python 2.4 will likely be dropped some time in the next year. --nate
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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------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online -------------------------------------------------------------
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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 -------------------------------------------------------------------------
John Powell (NIH/CIT) [E] 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)?
Hi John, There's no longer a need to run setup.sh, in fact this script has been removed from the most recent versions of Galaxy. The only thing you'll need to do is ensure that the newer version of the `python` command appears in front of any other `python`s in your $PATH: % export PATH=/usr/local/BIMAS/python_255/bin:$PATH % sh run.sh For persistance, set the PATH declaration in your shell's startup files (~/.bash_profile). --nate
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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participants (4)
-
John Powell (NIH/CIT) [E] -
Leandro Hermida -
Nate Coraor -
Pieter Neerincx