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.gruen...@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.gruen...@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 < >>>> 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 >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> https://lists.galaxyproject.org/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>> >> > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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