Great, still need to figure out why.
Thanks,
Bjoern
Am 27.11.2015 um 23:33 schrieb Jose Juan Almagro Armenteros:
Yes, I had that error but Devon Ryan point me out the solution in
this
thread:
https://biostar.usegalaxy.org/p/14989/. Now deepTools works
correctly for me.
Regards,
Jose
2015-11-27 22:01 GMT+01:00 Björn Grüning <bjoern.gruening(a)gmail.com>:
> Awesome!
>
> Sorry for the inconvenience ...!
> Is matplotlib installing for you? Can you confirm this error?
>
>
https://github.com/galaxyproject/tools-iuc/issues/417
>
> Thanks,
> Bjoern
>
> Am 27.11.2015 um 18:21 schrieb Jose Juan Almagro Armenteros:
>> Hello Bjoern,
>>
>> Yes, that solved the problem.
>>
>> Thank you!
>>
>> Regards,
>>
>> Jose
>>
>>
>>
>> 2015-11-27 17:59 GMT+01:00 Björn Grüning <bjoern.gruening(a)gmail.com>:
>>
>>> Hi Jose,
>>>
>>> can you please try to set:
>>>
>>> enable_beta_tool_command_isolation = True
>>>
>>> in your galaxy.ini file?
>>>
>>> Thanks,
>>> Bjoern
>>>
>>> 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
>>> last
>>>> version of deepTools (1.5.11.0) , as bamCompare or bamCorrelate.
> However,
>>>> when I run the same tools from the previous version (1.5.9.1.0), 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
>>>> eggs?
>>>>
>>>> 2015-11-27 13:03 GMT+01:00 Jose Juan Almagro Armenteros <
>>> jjalmagro(a)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 <
>>>>> jjalmagro(a)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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>>
>