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

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&gt;: > >> 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/

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&gt;: > 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&gt;: >>> >>>> 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/ >> >

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&gt;: > 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&gt;: >> >>> 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&gt;: >>>>> >>>>>> 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/ >>>> >>> >> >