So I have been trying to run the visualization workflow wmgx_vis. However, I keep getting an error that the workflow cannot produce a pdf with the character beta.
anadama2.util.ShellException: [Errno 43] Command `pandoc $PATH_INPUT/wmgx_report.md -o $PATH_OUTPUT/wmgx_report..pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone --toc' failed.
Out: b''
Err: b'Error producing PDF.\n
! Package inputenc Error: Unicode character \xce\xb2 (U+03B2)\n
(inputenc) not set up for use with LaTeX.\n\n
See the inputenc package documentation for explanation.\n
Type H <return> for immediate help.\n ... \n\n
l.360 dTDP-\xce\xb2-L-rhamnose biosynthesis}\n\n
Try running pandoc with --pdf-engine=xelatex.\n'
Basically, wmgx_vis calls pandoc in order to create a pdf. However, the character \xce\xb2, which is beta, is not recognized. I looked up where the call for pandoc is defined, and it is defined in anadama2/document.py.
# set the pandoc command based on if a table of contents will be included
pandoc_command="pandoc {0} -o {1} --variable=linkcolor:Blue "+\
"--variable=toccolor:Blue --pdf-engine=pdflatex --standalone"
I tried to call pandoc with --pdf-engine=xelatex instead of pdflatex. However, this solution didn’t work.
Any other solutions?