I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I'm guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don't believe takes arguments). My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported. -John run_scramble_script(): Executing in /home/galaxy/galaxy_dist/scripts/scramble/build/py2.4/python_daemon: /usr/bin/python -ES scramble.py Traceback (most recent call last): File "scramble.py", line 29, in ? execfile( "setup.py", globals(), locals() ) File "setup.py", line 22, in ? main_module = __import__(main_module_name, fromlist=['version']) TypeError: __import__() takes no keyword arguments scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/nose-0.11.1-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/WebOb-0.8.5-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/PasteScript-1.7.3-py2.4.egg Traceback (most recent call last): File "scripts/scramble.py", line 23, in ? eggs = c.scramble() File "/home/galaxy/galaxy_dist/lib/galaxy/eggs/scramble.py", line 243, in scramble raise last_exc # only 1 failure out of the crate, be more informative galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for python_daemon 1.5.5
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne <ozborn@uab.edu> wrote:
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I’m guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don’t believe takes arguments).
Sounds like a bug.
My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported.
There is currently a check to prevent Galaxy running on Python 2.7, but if you remove that at the very least you'll see lots of deprecation warnings. So we decided to go with Python 2.6 here. See also: https://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support I personally have no objection to Galaxy dropping support for Python 2.4 (in a timely manor to give existing users time to plan), it would give a bit more flexibility when writing tools for Galaxy. Peter
Peter Cock wrote:
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne <ozborn@uab.edu> wrote:
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I’m guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don’t believe takes arguments).
Sounds like a bug.
Yes, this is a bug. I'll work on it shortly.
My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported.
There is currently a check to prevent Galaxy running on Python 2.7, but if you remove that at the very least you'll see lots of deprecation warnings. So we decided to go with Python 2.6 here. See also: https://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support
I personally have no objection to Galaxy dropping support for Python 2.4 (in a timely manor to give existing users time to plan), it would give a bit more flexibility when writing tools for Galaxy.
Now that all modern popular operating systems I'm aware of ship at least 2.5, we will likely phase out 2.4 support. We haven't decided when this will be, but there will be a substantial amount of time between announcement and the end of support to allow adequate time to get upgraded. --nate
Peter
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Thanks Peter! I found 2.6 ( http://www.python.org/download/releases/2.6.6/) so I will go ahead and try that with galaxy and see if the problem goes away. -John On 2/2/11 12:07 PM, "Peter Cock" <p.j.a.cock@googlemail.com> wrote: On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne <ozborn@uab.edu> wrote:
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I'm guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don't believe takes arguments).
Sounds like a bug.
My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported.
There is currently a check to prevent Galaxy running on Python 2.7, but if you remove that at the very least you'll see lots of deprecation warnings. So we decided to go with Python 2.6 here. See also: https://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support I personally have no objection to Galaxy dropping support for Python 2.4 (in a timely manor to give existing users time to plan), it would give a bit more flexibility when writing tools for Galaxy. Peter
Sorry to dig up this old thread, but how do you remove the check that prevents galaxy running on 2.7? One of my developers just updated his workstation to Ubuntu 11.04 (Py 2.7) which is preventing him from running Galaxy. I'm not sure whether it would be better to remove this check or to just install 2.6 alongside 2.7. -- Branden Timm btimm@glbrc.wisc.edu On 2/2/2011 12:07 PM, Peter Cock wrote:
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne<ozborn@uab.edu> wrote:
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I’m guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don’t believe takes arguments). Sounds like a bug.
My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported. There is currently a check to prevent Galaxy running on Python 2.7, but if you remove that at the very least you'll see lots of deprecation warnings. So we decided to go with Python 2.6 here. See also: https://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support
I personally have no objection to Galaxy dropping support for Python 2.4 (in a timely manor to give existing users time to plan), it would give a bit more flexibility when writing tools for Galaxy.
Peter
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Branden Timm wrote:
Sorry to dig up this old thread, but how do you remove the check that prevents galaxy running on 2.7? One of my developers just updated his workstation to Ubuntu 11.04 (Py 2.7) which is preventing him from running Galaxy. I'm not sure whether it would be better to remove this check or to just install 2.6 alongside 2.7.
It's in galaxy-dist/scripts/check_python.py, and possibly other places. The last I heard, it does not work on 2.7, but I haven't investigated it myself. --nate
-- Branden Timm btimm@glbrc.wisc.edu
On 2/2/2011 12:07 PM, Peter Cock wrote:
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne<ozborn@uab.edu> wrote:
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I’m guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don’t believe takes arguments). Sounds like a bug.
My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported. There is currently a check to prevent Galaxy running on Python 2.7, but if you remove that at the very least you'll see lots of deprecation warnings. So we decided to go with Python 2.6 here. See also: https://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support
I personally have no objection to Galaxy dropping support for Python 2.4 (in a timely manor to give existing users time to plan), it would give a bit more flexibility when writing tools for Galaxy.
Peter
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participants (4)
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Branden Timm -
John David Osborne -
Nate Coraor -
Peter Cock