Tag as deprecated in the tool panels? RNA Structure Prediction 1.0

[jennaj]

toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0

EU: https://usegalaxy.eu/u/jenj/h/test-rna-structure-prediction

I            Traceback (most recent call last):
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/predict/predict_RNAs.py", line 11, in <module>
    from rtts_plot import *
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/predict/rtts_plot.py", line 6, in <module>
    import numpy as np
  File "/usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/core/__init__.py", line 5, in <module>
    import multiarray
ImportError: /usr/local/tools/numpy/1.7.1/iuc/package_numpy_1_7/028df1ddd7a2/lib/python/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_AsASCIIString

Then ORG seemingly resolves this, but the result is still a Python error.

             File "/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/predict/predict_RNAs.py", line 189
    print filepath
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(filepath)?

The tool is deprecated it seems https://github.com/search?q=repo%3Agalaxyproject%2Ftools-iuc%20rnastructure&type=code.

The tool shows up in tool panels at public servers as a valid choice. This is confusing for users. We should probably tag the tool as deprecated (integrated tool panel?) or correct it.

Thoughts?

End-users should choose a different tool for now.

[bernt-matthias]

This is not an IUC tool it seems. Owner is tyty. I will transfer the issue to the usegalaxy-tools repo.