Re: [galaxy-dev] Version Error and Python 2.7
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 > bt...@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 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 It looks like some eggs are getting out of date and when I run 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 > > > >___ > >galaxy-dev mailing list > >galaxy-dev@lists.bx.psu.edu > >http://lists.bx.psu.edu/listinfo/galaxy-dev > ___ > 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/ > ___ 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/
Re: [galaxy-dev] Version Error and Python 2.7
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 bt...@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 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 ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ 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/
Re: [galaxy-dev] Version Error and Python 2.7
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" wrote: On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne 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 ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Version Error and Python 2.7
Peter Cock wrote: > On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne 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 > > ___ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev > ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Version Error and Python 2.7
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne 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 ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
