I've recently updated my local instance of Galaxy from bitbucket to
git. It seems to work fine. No error when we run galaxy.
But I've been tried to cleanup datasets and when I ran this command :
universe_wsgi.ini -d 0 -1 -r $@
I have error in python module like this :
Traceback (most recent call last):
line 23, in <module>
File "/data/galaxy-dist/lib/galaxy/model/mapping.py", line 19, in <module>
from galaxy.model.custom_types import JSONType, MetadataType,
File "/data/galaxy-dist/lib/galaxy/model/custom_types.py", line 13,
from galaxy import app
File "/data/galaxy-dist/lib/galaxy/app.py", line 16, in <module>
from galaxy.visualization.data_providers.registry import
line 4, in <module>
from galaxy.visualization.data_providers import genome
line 15, in <module>
from bx.bbi.bigbed_file import BigBedFile
ImportError: No module named bigbed_file
I've already reinstall in galaxy virtual env lot of modules required
as bx-python , pyyaml, pysam, webhelpers...
But it's infinite and I don't understand why all python modules are
not retrieve while the galaxy instance works fine and I've had no
problem when I've updated the galaxy version.
How can I manage this problem and eventually re-install python, python
modules in virtual env ?
Thanks a lot.