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
Hi Ira, This has been reported before as well, but should be fixed without having to rescramble when we release our next dist-release soon. Thanks, K On Wed, Jun 22, 2011 at 12:47 AM, Ira Cooke <I.Cooke@latrobe.edu.au> 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
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participants (2)
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Ira Cooke -
Kanwei Li