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TurtleTools / caretta

A software-suite to perform multiple protein structure alignment and structure feature extraction.
BSD 3-Clause "New" or "Revised" License
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python 2.7 problem ? MacOS 11.1 #6

Closed 21tesla closed 3 years ago

21tesla commented 3 years ago

I just installed carretta manually on my Mac (MacOS 11.1). Can you suggest where the problem might be? Is my machine calling python2.7 by default instead of python3 ?

thank you

60 % caretta-cli test @> 2465 atoms and 1 coordinate set(s) were parsed in 0.02s. @> 2739 atoms and 1 coordinate set(s) were parsed in 0.02s. @> 2647 atoms and 1 coordinate set(s) were parsed in 0.02s. Found 3 PDB files @> 2465 atoms and 1 coordinate set(s) were parsed in 0.02s. @> 2739 atoms and 1 coordinate set(s) were parsed in 0.02s. @> 2647 atoms and 1 coordinate set(s) were parsed in 0.02s. Calculating pairwise distances... Constructing neighbor joining tree... Aligning [####################################] 100% Traceback (most recent call last): File "/Applications/Darwin/miniconda3/bin/caretta-cli", line 7, in exec(compile(f.read(), file, 'exec')) File "/Applications/Darwin/caretta/bin/caretta-cli", line 115, in app() File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/typer/main.py", line 214, in call return get_command(self)(*args, kwargs) File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(args, kwargs) File "/Applications/Darwin/miniconda3/lib/python3.8/site-packages/typer/main.py", line 497, in wrapper return callback(**use_params) # type: ignore File "/Applications/Darwin/caretta/bin/caretta-cli", line 97, in align multiple_alignment.StructureMultiple.align_from_pdb_files( File "/Applications/Darwin/caretta/caretta/multiple_alignment.py", line 295, in align_from_pdb_files msa_class.write_files( TypeError: write_files() got multiple values for argument 'only_dssp'

Ninjani commented 3 years ago

Thanks for bringing this to our attention. This ended up being an issue with the order of the arguments, we've fixed it now on master (commit ff2c2dd). Could you please reinstall and try again?

21tesla commented 3 years ago

Thank you. The CLI is functioning. I am still having issues loading files into the web app but it's not important if the command line app is working. Thank you again -Logan

Ninjani commented 3 years ago

Great! I'll open a new issue about the web app and close this one.