I want to install minipolish for polishing my assemblies after (minimap and miniasm). However when I try to install it gives the following error:
(base) dagobert@Mac-Pro-van-Dagobert ~ % pip install git+https://github.com/rrwick/Minipolish.git
Collecting git+https://github.com/rrwick/Minipolish.git
Cloning https://github.com/rrwick/Minipolish.git to /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-req-build-_xh4fbcg
Running command git clone --filter=blob:none --quiet https://github.com/rrwick/Minipolish.git /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-req-build-_xh4fbcg
Resolved https://github.com/rrwick/Minipolish.git to commit ee6b71ca5cd14d91b15ca0045637b4c15c3a4871
Preparing metadata (setup.py) ... done
Collecting edlib (from Minipolish==0.1.3)
Using cached edlib-1.3.9.tar.gz (91 kB)
Preparing metadata (setup.py) ... done
Building wheels for collected packages: Minipolish, edlib
Building wheel for Minipolish (setup.py) ... done
Created wheel for Minipolish: filename=Minipolish-0.1.3-py3-none-any.whl size=32324 sha256=078031039e2d1a2a45356d0a5489d0fbee08d218b8c3cef953adcd32c54d3abf
Stored in directory: /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-ephem-wheel-cache-nwoqy9bw/wheels/ec/cf/3c/7f59c40ef80ceb4b07ef6b04df5a73167176bac5eea32c269e
Building wheel for edlib (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
running bdist_wheel
running build
running build_ext
building 'edlib' extension
creating build
creating build/temp.macosx-11.1-arm64-cpython-312
creating build/temp.macosx-11.1-arm64-cpython-312/edlib
creating build/temp.macosx-11.1-arm64-cpython-312/edlib/src
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/dagobert/miniconda3/include -arch arm64 -fPIC -O2 -isystem /Users/dagobert/miniconda3/include -arch arm64 -Iedlib/include -I/Users/dagobert/miniconda3/include/python3.12 -c edlib.bycython.cpp -o build/temp.macosx-11.1-arm64-cpython-312/edlib.bycython.o -O3 -std=c++11
edlib.bycython.cpp:198:12: fatal error: 'longintrepr.h' file not found
include "longintrepr.h"
^~~~~~~~~~~~~~~
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 edlib
Running setup.py clean for edlib
Successfully built Minipolish
Failed to build edlib
ERROR: Could not build wheels for edlib, which is required to install pyproject.toml-based projects
So I guess I need edlib to install minipolish but when I look at the github instructions, it is a bit unclear to me (I am quite new to bioinformatics). Does anyone know how to install edlib and minipolish on a Mac Pro?
I want to install minipolish for polishing my assemblies after (minimap and miniasm). However when I try to install it gives the following error:
(base) dagobert@Mac-Pro-van-Dagobert ~ % pip install git+https://github.com/rrwick/Minipolish.git Collecting git+https://github.com/rrwick/Minipolish.git Cloning https://github.com/rrwick/Minipolish.git to /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-req-build-_xh4fbcg Running command git clone --filter=blob:none --quiet https://github.com/rrwick/Minipolish.git /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-req-build-_xh4fbcg Resolved https://github.com/rrwick/Minipolish.git to commit ee6b71ca5cd14d91b15ca0045637b4c15c3a4871 Preparing metadata (setup.py) ... done Collecting edlib (from Minipolish==0.1.3) Using cached edlib-1.3.9.tar.gz (91 kB) Preparing metadata (setup.py) ... done Building wheels for collected packages: Minipolish, edlib Building wheel for Minipolish (setup.py) ... done Created wheel for Minipolish: filename=Minipolish-0.1.3-py3-none-any.whl size=32324 sha256=078031039e2d1a2a45356d0a5489d0fbee08d218b8c3cef953adcd32c54d3abf Stored in directory: /private/var/folders/g4/0rpkxnq91_b38tsgwcqr75140000gn/T/pip-ephem-wheel-cache-nwoqy9bw/wheels/ec/cf/3c/7f59c40ef80ceb4b07ef6b04df5a73167176bac5eea32c269e Building wheel for edlib (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [14 lines of output] running bdist_wheel running build running build_ext building 'edlib' extension creating build creating build/temp.macosx-11.1-arm64-cpython-312 creating build/temp.macosx-11.1-arm64-cpython-312/edlib creating build/temp.macosx-11.1-arm64-cpython-312/edlib/src clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/dagobert/miniconda3/include -arch arm64 -fPIC -O2 -isystem /Users/dagobert/miniconda3/include -arch arm64 -Iedlib/include -I/Users/dagobert/miniconda3/include/python3.12 -c edlib.bycython.cpp -o build/temp.macosx-11.1-arm64-cpython-312/edlib.bycython.o -O3 -std=c++11 edlib.bycython.cpp:198:12: fatal error: 'longintrepr.h' file not found
include "longintrepr.h"
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for edlib Running setup.py clean for edlib Successfully built Minipolish Failed to build edlib ERROR: Could not build wheels for edlib, which is required to install pyproject.toml-based projects
So I guess I need edlib to install minipolish but when I look at the github instructions, it is a bit unclear to me (I am quite new to bioinformatics). Does anyone know how to install edlib and minipolish on a Mac Pro?
Thanks!