Multiqc: Errors in --help and --version when run in bioconductor docker image.

[Drwhit]

Description of bug:
multiqc installed, but both --help and --version commands result in the following error log.

MultiQC Error log:

~$ ~/.local/bin/multiqc --version
Traceback (most recent call last):
  File "/home/rstudio/.local/bin/multiqc", line 32, in <module>
    from multiqc.plots import table
  File "/home/rstudio/.local/lib/python2.7/site-packages/multiqc/plots/table.py", line 9, in <module>
    from multiqc.utils import config, report, util_functions, mqc_colour
  File "/home/rstudio/.local/lib/python2.7/site-packages/multiqc/utils/mqc_colour.py", line 7, in <module>
    import spectra
  File "/home/rstudio/.local/lib/python2.7/site-packages/spectra/__init__.py", line 1, in <module>
    from .core import COLOR_SPACES, Color, Scale
  File "/home/rstudio/.local/lib/python2.7/site-packages/spectra/core.py", line 1, in <module>
    from colormath import color_objects, color_conversions
  File "/home/rstudio/.local/lib/python2.7/site-packages/colormath/color_conversions.py", line 167, in <module>
    def Spectral_to_XYZ(cobj, illuminant_override=None, *args, **kwargs):
  File "/home/rstudio/.local/lib/python2.7/site-packages/colormath/color_conversions.py", line 159, in decorator
    _conversion_manager.add_type_conversion(start_type, target_type, f)
  File "/home/rstudio/.local/lib/python2.7/site-packages/colormath/color_conversions.py", line 125, in add_type_conversion
    self.conversion_graph.add_edge(start_type, target_type, {'conversion_function': conversion_function})
TypeError: add_edge() takes exactly 3 arguments (4 given)

• Command used to run MultiQC
  
  
  
  • multiqc --version
  
  
• MultiQC Version:
  
  
  
  • v1.0 and v1.2
  
  
• Operating System:
  
  
  
  • bioconductor docker image running on macOS Sierra 10.12.5
  
  
• Python Version:
  
  
  
  • Python 2.7.13
  
  
• Method of MultiQC installation:
  
  
  
  • all of the following result in the same problem: pip install --user multiqc, pip install multiqc, pip install --user multiqc==1.0
  
  

[ewels]

Thanks @Drwhit,

This is a known bug (see #592 and several others). It's been fixed in 1.3dev of MultiQC for some time but only recently have the downstream dependencies properly released new versions, making this a more immediate problem.

I'm hoping to get 1.3 released soon (today if all goes to plan) at which time this will resolve itself. In the mean time, installing using conda should work (conda install -c bioconda multiqc) as the dependency is patched or you can install the development version using pip:

pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git

Phil