Question: plotCorrelation and pandas error
0
gravatar for maryjoazzi
7 months ago by
maryjoazzi0
maryjoazzi0 wrote:

Hey I am using plotCorrelation and I get the following error

  File "/home/pk3/galaxy/database/dependencies/_conda/envs/mulled-v1-5ba2c93da92160ba380ae3d57d5da01827e12a494c86cf50e7e386136c8c12c2/lib/python3.6/site-packages/plotly/figure_factory/_county_choropleth.py", line 8, in 
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

so i made sure that pandas was in fact installed and then I went into the "_county_choropleth.py" file and added:

import sys
sys.path.insert(0,"mydirectory")
import pandas as pd

and now im getting the following error:

 File "/home/pk3/galaxy/database/dependencies/_conda/envs/mulled-v1-5ba2c93da92160ba380ae3d57d5da01827e12a494c86cf50e7e386136c8c12c2/lib/python3.6/site-packages/plotly/figure_factory/_county_choropleth.py", line 9, in 
    import pandas as pd
  File "/usr/local/lib/python2.7/dist-packages/pandas/__init__.py", line 35, in 
    "the C extensions first.".format(module))
ImportError: C extension: /usr/local/lib/python2.7/dist-packages/pandas/_libs/tslib.so: undefined symbol: _Py_ZeroStruct not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext --inplace --force' to build the C extensions first.

any suggestions on how/what to fix?

ADD COMMENTlink modified 7 months ago by Bjoern Gruening5.1k • written 7 months ago by maryjoazzi0

This is using deeptools3 isn't it?

ADD REPLYlink written 7 months ago by Bjoern Gruening5.1k
2
gravatar for Bjoern Gruening
7 months ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

This was fixed upstream. If you remove your conda environment and let Galaxy install a new one this should work.

Thanks to Devon for the fix!

Bjoern

ADD COMMENTlink written 7 months ago by Bjoern Gruening5.1k

All is fixed!Thankyou!

ADD REPLYlink written 7 months ago by maryjoazzi0
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