I bit more of information. I have this problem running tools from the last
version of deepTools ( , as bamCompare or bamCorrelate. However,
when I run the same tools from the previous version (, they work
correctly. I have reinstalled this last version but nothing. Is it possible
that, as these two versions are using different numpy versions, bx-python
is using the version from the deepTools package and not the one from the

2015-11-27 13:03 GMT+01:00 Jose Juan Almagro Armenteros <jjalma...@gmail.com

> I have tried to remove the bx-python and numpy eggs and then I have
> fetched them again but this didn't work neither.
> Any idea why bx-python is not recognizing the proper numpy version?
> Regards,
> Jose
> 2015-11-27 0:53 GMT+01:00 Jose Juan Almagro Armenteros <
> jjalma...@gmail.com>:
>> Hello,
>> I am in the master branch and I recently pull all the changes to my local
>> Galaxy. However, when I run one tool I obtained this error:
>> Fatal error: Matched on Error:
>> Traceback (most recent call last):
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/024/24973/set_metadata_GULyCa.py",
>>  line 1, in <module>
>>     from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py",
>>  line 27, in <module>
>>     import galaxy.model.mapping  # need to load this before we unpickle, in 
>> order to setup properties assigned by the mappers
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/model/mapping.py", 
>> line 21, in <module>
>>     from galaxy.model.custom_types import JSONType, MetadataType, 
>> TrimmedString, UUIDType
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py",
>>  line 15, in <module>
>>     from galaxy import app
>>   File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 
>> 14, in <module>
>>     from galaxy.visualization.data_providers.registry import 
>> DataProviderRegistry
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
>>  line 2, in <module>
>>     from galaxy.visualization.data_providers import genome
>>   File 
>> "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
>>  line 16, in <module>
>>     from bx.bbi.bigbed_file import BigBedFile
>>   File "bigbed_file.pyx", line 1, in init bx.bbi.bigbed_file 
>> (lib/bx/bbi/bigbed_file.c:6272)
>>   File "numpy.pxd", line 155, in init bx.bbi.bbi_file 
>> (lib/bx/bbi/bbi_file.c:12669)
>> ValueError: numpy.dtype has the wrong size, try recompiling
>> I suppose there is a problem with the bx-python or numpy egg but I am not
>> really sure if is this. I run check_eggs.py and it did nothing and I also
>> try to update numpy for the system, which didn't work neither.
>> Do you know which numpy should I recompile in order to get this to work?
>> Regards,
>> Jose
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