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Teichlab / cellphonedb

MIT License
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Error: no such option: --counts-data #258

Open 10adavis opened 3 years ago

10adavis commented 3 years ago

After specifying "--counts-data=gene_name", I am receiving the message: "Error: no such option: --counts-data"

This seems to be a problem specific to running on Windows 10 using the Anaconda Powershell prompt, as it works fine when running on Ubuntu. Any way to specify --counts-data for Windows?

dienerpatrick commented 3 years ago

I have the exact same problem!

Lovelock1998 commented 2 years ago

I have the exact same problem......

prete commented 2 years ago

This seems to be a known Windows issue, are you both on Windows as well? Could you also provide the full command you're using to launch CellPhoneDB, please?

Lovelock1998 commented 2 years ago

This seems to be a known Windows issue, are you both on Windows as well? Could you also provide the full command you're using to launch CellPhoneDB, please?

I use data from 'Seurat' tutorial dataset pbmc which contains 2700 single cells.The command is run on windows.Look forward to your reply.Thank u. image

bhavyaac commented 2 years ago

Not sure if this will help anyone in this thread, but I would like to share my experience with this error. I am using a Linux system (on a compute cluster), not Windows.

TL;DR it may help to check that your CellphoneDB version is correct, and that your dependencies have installed properly.

I got this error, and it turns out that I had some sort of issue with rpy2 installation (like some Windows users had experienced e.g. #184), and this may be the reason that I found CellphoneDB version 1.1.0 had been installed instead of 2.1.7 (like in issue #338). This makes sense, because I believe the --counts-data argument was not introduced yet in version 1.1.0. I solved this by ensuring that my python and pip paths were correct i.e. within my virtual environment (e.g. which pip), and that you have at least Python 3.6 (run python --version, and the virtual environment was also created in Python >= 3.6). Once I had checked this, I installed the desired version of CellphoneDB with pip install cellphonedb==2.1.7 --no-deps in order to avoid the dependency conflict from before. Then, I installed each line of requirements.txt individually using pip install "boto3>=1.7,<1.7.99" for example. (Note: I had to install Cython before installing scikit-learn.) Now, I was able to run CellphoneDB 2.1.7 normally. I hope this makes sense. I'm a novice to virtual environments and python installations, so I would appreciate feedback as well!