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 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@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
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@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@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
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@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@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/
Hello Bjoern,
Yes, that solved the problem.
Thank you!
Regards,
Jose
2015-11-27 17:59 GMT+01:00 Björn Grüning bjoern.gruening@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@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@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 weunpickle, 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 appFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 14, in <module>
from galaxy.visualization.data_providers.registry importDataProviderRegistry
File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module>
from galaxy.visualization.data_providers import genomeFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 16, in <module>
from bx.bbi.bigbed_file import BigBedFileFile "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/
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@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@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@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 weunpickle, 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 appFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 14, in <module>
from galaxy.visualization.data_providers.registry importDataProviderRegistry
File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module>
from galaxy.visualization.data_providers import genomeFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 16, in <module>
from bx.bbi.bigbed_file import BigBedFileFile "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@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@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@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@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 weunpickle, 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 appFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line
14,
in <module>
from galaxy.visualization.data_providers.registry importDataProviderRegistry
File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
line 2, in <module>
from galaxy.visualization.data_providers import genomeFile
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
line 16, in <module>
from bx.bbi.bigbed_file import BigBedFileFile "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/
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@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@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@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@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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Björn Grüning -
Jose Juan Almagro Armenteros