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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