I was trying to update my existing Galaxy installation to the latest release (50e249442c5a) and encounter the following when I start it up: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 11, in ? from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in ? from galaxy.web.base.controller import UsesHistory File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in ? from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 13, in ? from galaxy.datatypes.util.gff_util import * File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 152 finally: ^ SyntaxError: invalid syntax I have attached the full script of what I did. I'm not too familiar with Mercurial and couldn't find any guidance in the wiki or mailing list on exactly what choices to make when Mercurial encountered conflicts, so I accepted the "delete" or "other" options when these occurred. Any help would be appreciated. Thanks, Olen
Olen, This is a runtime error, not an update error; it is occurring because we mistakenly committed code that is not compliant with python 2.4 Here are your options to fix this error: (1) update your python version from 2.4 to 2.5 or 2.6; (2) update your installation from galaxy-central; specifically, you'll need changeset 5370:1cb94990d839 (3) make the changes in changeset manually: https://bitbucket.org/galaxy/galaxy-central/changeset/1cb94990d839 and then merge when the next update comes out. Sorry for the inconvenience. J. On Apr 18, 2011, at 5:58 PM, Olen Vance Sluder Jr wrote:
I was trying to update my existing Galaxy installation to the latest release (50e249442c5a) and encounter the following when I start it up:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 11, in ? from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in ? from galaxy.web.base.controller import UsesHistory File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in ? from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 13, in ? from galaxy.datatypes.util.gff_util import * File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 152 finally: ^ SyntaxError: invalid syntax
I have attached the full script of what I did. I'm not too familiar with Mercurial and couldn't find any guidance in the wiki or mailing list on exactly what choices to make when Mercurial encountered conflicts, so I accepted the "delete" or "other" options when these occurred.
Any help would be appreciated.
Thanks, Olen <update.out>___________________________________________________________ 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:
On Mon, Apr 18, 2011 at 6:27 PM, Jeremy Goecks wrote:
This is a runtime error, not an update error; it is occurring because we mistakenly committed code that is not compliant with python 2.4
Yes, sorry: you're technically correct. I should have said "Problem after update" in my subject. ;-)
Here are your options to fix this error: (1) update your python version from 2.4 to 2.5 or 2.6;
Unfortunately, not an option: I am trying to keep my CentOS 5 compatible with the downstream vendor and Python 2.4.3 is the installed version.
(2) update your installation from galaxy-central; specifically, you'll need changeset 5370:1cb94990d839
My preference, but as I said in my original post, I'm not too familiar with Mercurial, so what is the syntax for pulling a single changeset from a repository from other than from where I originally "cloned"? I tried: hg pull -u -r 5370:1cb94990d839 https://bitbucket.org/galaxy/galaxy-central and got: abort: unknown revision '5370:1cb94990d839'! When I dropped the "5370:", I got 15 changesets and it wanted a database upgrade when I restarted. Luckily, I was testing on a copy.
Sorry for the inconvenience.
No worries. -- Olen
participants (2)
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Jeremy Goecks -
Olen Vance Sluder Jr