Hello Kanwei, I'm fairly certain I downloaded the .tar.gz from sourceforge and installed numpy that way. Can this be causing a problem? Thanks for your help Roger On Tue, Jul 20, 2010 at 3:50 PM, Kanwei Li <kanwei@gmail.com> wrote:
Hi Roger,
Do you have that numpy installed on your system through something like easy_install? It might be conflicting with the numpy egg that we provide.
-Kanwei
On Tue, Jul 20, 2010 at 3:42 PM, Roger Kapul <rkapul@gmail.com> wrote:
Hello,
I'm running a fresh install of Ubuntu 10.04 LTS, python version 2.6 and numpy version 1.3.0 and I get this error when I try to run galaxy on my machine. I downloaded and installed galaxy by following the steps on the wiki and used the mercurial repository to download it.
galaxy.web.framework.base DEBUG 2010-07-20 12:36:28,494 Enabling 'async' controller, class: ASync Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run invoke(command, command_name, options, args[1:]) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke exit_code = runner.run(args) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run result = self.command() File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 276, in command relative_to=base, global_conf=vars) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 313, in loadapp **kw) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 225, in loadobj return context.create() File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 625, in create return self.object_type.invoke(self) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File
"/home/roger/galaxy-python/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py",
line 57, in fix_call val = callable(*args, **kw) File "/home/roger/galaxy-python/galaxy_dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/home/roger/galaxy-python/galaxy_dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File
"/home/roger/galaxy-python/galaxy_dist/lib/galaxy/web/controllers/tracks.py",
line 27, in <module> from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider File
"/home/roger/galaxy-python/galaxy_dist/lib/galaxy/visualization/tracks/data/array_tree.py",
line 8, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
Any advice?
Thank you Roger
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