Yes, that solved the problem.
2015-11-27 17:59 GMT+01:00 Björn Grüning <bjoern.gruening(a)gmail.com>:
can you please try to set:
enable_beta_tool_command_isolation = True
in your galaxy.ini file?
Am 27.11.2015 um 16:01 schrieb Jose Juan Almagro Armenteros:
> I bit more of information. I have this problem running tools from the
> version of deepTools (22.214.171.124) , as bamCompare or bamCorrelate. However,
> when I run the same tools from the previous version (126.96.36.199.0), they
> correctly. I have reinstalled this last version but nothing. Is it
> 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 <
>> 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?
>> 2015-11-27 0:53 GMT+01:00 Jose Juan Almagro Armenteros <
>>> I am in the master branch and I recently pull all the changes to my
>>> Galaxy. However, when I run one tool I obtained this error:
>>> Fatal error: Matched on Error:
>>> Traceback (most recent call last):
line 1, in <module>
>>> from galaxy_ext.metadata.set_metadata import set_metadata;
line 27, in <module>
>>> import galaxy.model.mapping # need to load this before we
unpickle, in order to setup properties assigned by the mappers
line 21, in <module>
>>> from galaxy.model.custom_types import JSONType, MetadataType,
line 15, in <module>
>>> from galaxy import app
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 14,
>>> from galaxy.visualization.data_providers.registry import
line 2, in <module>
>>> from galaxy.visualization.data_providers import genome
line 16, in <module>
>>> from bx.bbi.bigbed_file import BigBedFile
>>> File "bigbed_file.pyx", line 1, in init bx.bbi.bigbed_file
>>> File "numpy.pxd", line 155, in init bx.bbi.bbi_file
>>> 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
>>> really sure if is this. I run check_eggs.py and it did nothing and I
>>> 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
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