Good to know that I'm not the only one.
Also, I didn't put the rescramble commands in my original email ( In case there are other mac users googling this thread).
cd galaxy-dist/scripts/ rm -r ../eggs/numpy-1.3.0-py2.6-macosx-10.6-universal-ucs2.egg rm -r ../eggs/bx_python-0.7.0_494c2d1d68b3-py2.6-macosx-10.6-universal-ucs2.egg python scramble.py numpy python scramble.py bx_python
Of course, you also need developer tools installed.
Ira
On 23/06/2011, at 2:16 AM, Michael Steder wrote:
Hi Ira,
I had the same problem and scrambling the eggs myself seemed to be the workaround.
I'm not sure why we're having problems. It does seem to be specific to mac though, as I can run this same checkout on linux without any workarounds.
~Mike
On Jun 21, 2011, at 11:47 PM, Ira Cooke wrote:
Hi,
I recently downloaded galaxy and had some problems installing it on my machine (running Mac OSX 10.6.7 ). I've found a workaround to my problem, but I thought I should post here in case it is useful.
I obtained the standard galaxy distribution using
hg clone https://bitbucket.org/galaxy/galaxy-dist/
I then tried running sh run.sh but got;
Traceback (most recent call last): File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, 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
I googled this error and found a post suggesting that I try virtualenv ... I tried that but it made no difference.
Python --version returns 2.6.1
After some digging I tried rescrambling the numpy and then the bx_python egg. After rescrambling the latter sh run.sh worked.
Anyway I'm not sure if other mac users have had similar problems. In my case I'm pretty sure I had installed things with easy_install in the past ...but I assume using virtualenv would have solved that problem.
Ira
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: