Closed emrullahub closed 2 years ago
Hi Emrullah,
The documentation on the website is a outdated in comparison to the newest PCAngsd version. So you would also need to do the following:
# Enter PCAngsd folder
cd pcangsd
pip3 install -e .
Now you should use PCAngsd by simply calling pcangsd --beagle path/input.gz --out test
in the terminal.
Let me know if that works.
Best, Jonas
Hi,
It worked, your code downloaded the pcangsd library.
Thank you, Emrullah
hello! Dear Rosemeis, I met the same problem that "reader_cy" cannot be imported. I tried your above suggestions, but it didn't work . Can you do me a favor? thanks
This seems to be an issue with your systems compiler versions: https://github.com/stan-dev/pystan/issues/294
This seems to be an issue with your systems compiler versions: stan-dev/pystan#294
Thank you for your quick reply. I've probably read the link you gave. Because I'm not very good at CS and bioinfor., it looks a little difficult. overall, thank you for your reply. I'll try my best to solve it, or try it on another computer.
No problem. :-) A potential fix could be by installing the following in your conda environment:
conda install c-compiler cxx-compiler
And then try to remove and reinstall pcangsd. Let me know if that works.
Best, Jonas
Thanks a lot! I installed these two packages you suggested, and reinstalled pcangsd. Your suggestions worked! thanks again for solving my problem. (sorry for late reply).
1. conda install -c conda-forge c-compiler
2. conda install -c conda-forge cxx-compiler
3. git clone https://github.com/Rosemeis/pcangsd.git
4. cd pcangsd/
5. python setup.py build_ext --inplace
6. pip install --user -r requirements.txt
7. pip3 install -e .
That is great to hear! :-)
Hi @Rosemeis
I am having the exact same problem with cython, and I tried all the solutions suggested above (as well as installing cython separately, making a separate python environment aligning with the cython version) but none of these have worked for me...
When I run "pip install --user -r requirements.txt" the response is: "Requirement already satisfied: cython"
However, when I do the next step "pip3 install -e ." it says "ModuleNotFoundError: No module named 'Cython'"
I think this is why I try running pcangsd I get the error message "ImportError: cannot import name 'reader_cy' from 'pcangsd' "
Not sure how else to proceed....If you have any further guidance I would be super grateful for that!
Hi @AstridAlexAndersson
I think it might be due to two different python installations, where "pip" and "pip3" is calling different ones. Can you try reinstalling while using the first step with "pip3":
git clone https://github.com/Rosemeis/pcangsd.git
cd pcangsd
pip3 install --user -r requirements.txt
python setup.py build_ext --inplace
pip3 install -e .
Best, Jonas
Hi Jonas,
Thank you for your suggestion. I agree it must be some sort of version mismatch, but when I tried reinstalling with pip3 I still receive the same errors ☹
Greatly appreciate your input, Astrid
From: Jonas Meisner @.> Reply to: Rosemeis/pcangsd @.> Date: Friday, 19 May 2023 at 2:43 PM To: Rosemeis/pcangsd @.> Cc: @." @.>, Mention @.> Subject: Re: [Rosemeis/pcangsd] Cythonized pcangsd.py not working (Issue #61)
Hi @AstridAlexAnderssonhttps://github.com/AstridAlexAndersson
I think it might be due to two different python installations, where "pip" and "pip3" is calling different ones. Can you try reinstalling while using the first step with "pip3":
pip3 install --user -r requirements.txt
git clone https://github.com/Rosemeis/pcangsd.git
cd pcangsd
python setup.py build_ext --inplace
pip3 install -e .
Best, Jonas
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Hi, i did cythonize process with this code "python3 setup.py build_ext --inplace" but i am getting the following error when im trying to do pca with test data on pcangsd website:
PCAngsd v.1.10. Jonas Meisner and Anders Albrechtsen. Using 64 thread(s).
Traceback (most recent call last): File "pcangsd/pcangsd/pcangsd.py", line 455, in
main()
File "pcangsd/pcangsd/pcangsd.py", line 148, in main
from pcangsd import reader_cy
ImportError: cannot import name 'reader_cy' from 'pcangsd' (/home/emr/pcangsd/pcangsd/pcangsd.py)
Can you help me how to solve it? Thanks, Emrullah