search

TAMU-CPT / CPT-ToolshedSource

1 stars 1 forks source link

Genome mapper #10

Closed curtisim0 closed 1 month ago

curtisim0 commented 3 months ago

Fix the "linear genome plot" tool

jasonjgill commented 3 months ago

Error message when I tried to run Linear Genome Plot:

Traceback (most recent call last): File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/linear_genome_plot.py", line 3, in from dna_features_viewer import BiopythonTranslator, GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/init.py", line 3, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/init.py", line 1, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py", line 9, in from .BokehPlottableMixin import BokehPlottableMixin File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py", line 10, in import pandas as pd File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/init.py", line 180, in import pandas.testing File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/testing.py", line 5, in from pandas._testing import ( File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/_testing.py", line 24, in import pandas._libs.testing as _testing File "pandas/_libs/testing.pyx", line 10, in init pandas._libs.testing File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(__former_attrs_[attr]) AttributeError: module 'numpy' has no attribute 'bool'. np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool` here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

jasonjgill commented 2 months ago

Bjorn says the tool should be updated but when I tested it i got a similar error as before:

Traceback (most recent call last): File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/linear_genome_plot.py", line 3, in from dna_features_viewer import BiopythonTranslator, GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/init.py", line 3, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/init.py", line 1, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py", line 9, in from .BokehPlottableMixin import BokehPlottableMixin File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py", line 10, in import pandas as pd File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/init.py", line 180, in import pandas.testing File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/testing.py", line 5, in from pandas._testing import ( File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/pandas/_testing.py", line 24, in import pandas._libs.testing as _testing File "pandas/_libs/testing.pyx", line 10, in init pandas._libs.testing File "/usr/local/tools/_conda/envs/mulled-v1-8de2d0da844e361b56c1dfd483800bfb038c8ce53b2199ddbf35b15cec318162/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(__former_attrs_[attr]) AttributeError: module 'numpy' has no attribute 'bool'. np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool` here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

curtisim0 commented 2 months ago

Let me double check, but that should no longer be the case. Smells like cache.

curtisim0 commented 2 months ago

Okay, I did a "resync" as I had a small diff on local. But, I do believe it is a caching thing or something. There's no mentions of pandas in this tool, besides a deep dependency that try/excepts to see if it's available.

IE, this error can't be raised unless it's pulling a previous version/sha (from what I can tell).

jasonjgill commented 2 months ago

Is caching even a thing in the toolshed? I will ask Bjorn to run the update from the toolshed again.

jasonjgill commented 2 months ago

ran it again got a different error:

Traceback (most recent call last): File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/linear_genome_plot.py", line 3, in from dna_features_viewer import BiopythonTranslator, GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/init.py", line 3, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/init.py", line 1, in from .GraphicRecord import GraphicRecord File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py", line 16, in from .MatplotlibPlottableMixin import MatplotlibPlottableMixin File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/cpt/cpt_linear_genome_plot/e923c686ead9/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py", line 5, in import matplotlib.pyplot as plt ModuleNotFoundError: No module named 'matplotlib'

curtisim0 commented 2 months ago

hmmmm matplotlib is part of the dependencies.

Can you confirm that the dependencies are resolved on the eu galaxy?