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 last version of deepTools (126.96.36.199) , as bamCompare or bamCorrelate. However, when I run the same tools from the previous version (188.8.131.52.0), 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 <firstname.lastname@example.org
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 < email@example.com>:
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?
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