Installation graphlan

[Shwetha_Kumar]

I am not sure this has been quite answered in the previous posts as well. I have this issue with installing graphaln. I get this error.

include/python3.12 -c Bio/triemodule.c -o build/temp.macosx-10.9-x86_64-cpython-312/Bio/triemodule.o
Bio/triemodule.c:837:25: error: expression is not assignable
Py_TYPE(&Trie_Type) = &PyType_Type;
~~~~~~~~~~~~~~~~~~~ ^
1 error generated.
error: command ‘/usr/bin/clang’ failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for biopython
Running setup.py clean for biopython
Failed to build biopython
ERROR: Could not build wheels for biopython, which is required to install pyproject.toml-based projects

[sagunmaharjann]

Hi @Shwetha_Kumar ,
Thank you for reaching out to the bioBakery Lab. Can you please try the conda graphlan installation rather than PyPi please? It looks like a compile install issue on the PyPi side.

Regards,
Sagun

[Shwetha_Kumar]

I think I tried installing using

. I think there are compatibility issues because the package needs dependencies from two versions of python (that’s what I understood). I think this was posted as an issue on the repo

Error in installing graphlan

[Samantha]

I’m not an admin here, but I ran into the same error you had with the conda install. I seem to have gotten around it by making a new conda environment with Python 2.7:

conda create -n graphlan2.7 python=2.7
conda activate graphlan2.7
conda install -c bioconda graphlan

This allowed the install to go through for me, hopefully it works for you as well!

~Samantha

[Shwetha_Kumar]

Thank you, so much. This helped and i was able to get it installed…

Thank you