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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
305 stars 52 forks source link

cannot install/use cellphonedb #103

Closed fabioark closed 1 year ago

fabioark commented 1 year ago

Hi,

I'm having trouble installing (or use) CellPhoneDB. I install with : 1: conda create -n cpdb python=3.8 2: conda activate cpdb 3: pip install cellphonedb and I get the following output:

Collecting cellphonedb Using cached CellphoneDB-4.0.0-py3-none-any.whl (66 kB) Requirement already satisfied: ktplotspy>=0.1.4 in ./.local/lib/python3.8/site-packages (from cellphonedb) (0.1.9) Requirement already satisfied: numpy>=1.21.6 in ./.local/lib/python3.8/site-packages (from cellphonedb) (1.24.2) Requirement already satisfied: anndata>=0.8 in ./.local/lib/python3.8/site-packages (from cellphonedb) (0.8.0) Requirement already satisfied: requests>=2.25 in ./.local/lib/python3.8/site-packages (from cellphonedb) (2.28.2) Requirement already satisfied: scikit-learn==0.24 in ./.local/lib/python3.8/site-packages (from cellphonedb) (0.24.0) Requirement already satisfied: numpy-groupies>=0.9.15 in ./.local/lib/python3.8/site-packages (from cellphonedb) (0.9.20) Requirement already satisfied: geosketch==1.2 in ./.local/lib/python3.8/site-packages (from cellphonedb) (1.2) Requirement already satisfied: pandas>=1.5.0 in ./.local/lib/python3.8/site-packages (from cellphonedb) (1.5.3) Requirement already satisfied: tqdm<5.0,>=4.3 in ./.local/lib/python3.8/site-packages (from cellphonedb) (4.62.3) Requirement already satisfied: plotnine in ./.local/lib/python3.8/site-packages (from ktplotspy>=0.1.4->cellphonedb) (0.10.1) Requirement already satisfied: python-circos<0.4.0,>=0.3.0 in ./.local/lib/python3.8/site-packages (from ktplotspy>=0.1.4->cellphonedb) (0.3.0) Requirement already satisfied: seaborn in ./.local/lib/python3.8/site-packages (from ktplotspy>=0.1.4->cellphonedb) (0.12.2) Requirement already satisfied: scipy>1.4 in ./.local/lib/python3.8/site-packages (from anndata>=0.8->cellphonedb) (1.10.1) Requirement already satisfied: h5py>=3 in ./.local/lib/python3.8/site-packages (from anndata>=0.8->cellphonedb) (3.8.0) Requirement already satisfied: natsort in ./.local/lib/python3.8/site-packages (from anndata>=0.8->cellphonedb) (8.3.0) Requirement already satisfied: packaging>=20 in ./.local/lib/python3.8/site-packages (from anndata>=0.8->cellphonedb) (23.0) Requirement already satisfied: charset-normalizer<4,>=2 in ./.local/lib/python3.8/site-packages (from requests>=2.25->cellphonedb) (3.0.1) Requirement already satisfied: idna<4,>=2.5 in /usr/lib/python3/dist-packages (from requests>=2.25->cellphonedb) (2.8) Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/python3/dist-packages (from requests>=2.25->cellphonedb) (2019.11.28) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/lib/python3/dist-packages (from requests>=2.25->cellphonedb) (1.25.8) Requirement already satisfied: joblib>=0.11 in ./.local/lib/python3.8/site-packages (from scikit-learn==0.24->cellphonedb) (1.2.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.local/lib/python3.8/site-packages (from scikit-learn==0.24->cellphonedb) (3.1.0) Requirement already satisfied: fbpca>=1.0 in ./.local/lib/python3.8/site-packages (from geosketch==1.2->cellphonedb) (1.0) Requirement already satisfied: python-dateutil>=2.8.1 in ./.local/lib/python3.8/site-packages (from pandas>=1.5.0->cellphonedb) (2.8.2) Requirement already satisfied: pytz>=2020.1 in ./.local/lib/python3.8/site-packages (from pandas>=1.5.0->cellphonedb) (2022.7.1) Requirement already satisfied: mizani>=0.8.1 in ./.local/lib/python3.8/site-packages (from plotnine->ktplotspy>=0.1.4->cellphonedb) (0.8.1) Requirement already satisfied: patsy>=0.5.1 in ./.local/lib/python3.8/site-packages (from plotnine->ktplotspy>=0.1.4->cellphonedb) (0.5.3) Requirement already satisfied: matplotlib>=3.5.0 in ./.local/lib/python3.8/site-packages (from plotnine->ktplotspy>=0.1.4->cellphonedb) (3.7.0) Requirement already satisfied: statsmodels>=0.13.2 in ./.local/lib/python3.8/site-packages (from plotnine->ktplotspy>=0.1.4->cellphonedb) (0.13.5) Requirement already satisfied: biopython>=1.78 in ./.local/lib/python3.8/site-packages (from python-circos<0.4.0,>=0.3.0->ktplotspy>=0.1.4->cellphonedb) (1.79) Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.1->pandas>=1.5.0->cellphonedb) (1.14.0) Requirement already satisfied: backports.zoneinfo; python_version < "3.9" in ./.local/lib/python3.8/site-packages (from mizani>=0.8.1->plotnine->ktplotspy>=0.1.4->cellphonedb) (0.2.1) Requirement already satisfied: palettable in ./.local/lib/python3.8/site-packages (from mizani>=0.8.1->plotnine->ktplotspy>=0.1.4->cellphonedb) (3.3.0) Requirement already satisfied: pyparsing>=2.3.1 in /usr/lib/python3/dist-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (2.4.6) Requirement already satisfied: kiwisolver>=1.0.1 in /usr/lib/python3/dist-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (1.0.1) Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (7.0.0) Requirement already satisfied: cycler>=0.10 in /usr/lib/python3/dist-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (0.10.0) Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (4.38.0) Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (1.0.7) Requirement already satisfied: importlib-resources>=3.2.0; python_version < "3.10" in ./.local/lib/python3.8/site-packages (from matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (5.12.0) Requirement already satisfied: zipp>=3.1.0; python_version < "3.10" in ./.local/lib/python3.8/site-packages (from importlib-resources>=3.2.0; python_version < "3.10"->matplotlib>=3.5.0->plotnine->ktplotspy>=0.1.4->cellphonedb) (3.15.0) Installing collected packages: cellphonedb Successfully installed cellphonedb-4.0.0

but when I run ： cellphonedb --help the output is:

cellphonedb: command not found

I'm using windows to remotely connect to the server，I believe this maybe a boo-boo but I really got stuck with this problem for three days and haven't been able to fix it

I'd be really grateful if anyone could offer any advice. I am also happy to provide more information if needed.

fabioark commented 1 year ago

An update of my recent thought: It seems that cellphonedb 4.0.0 is, instead of a command, a python package that its usage is demonstrated in tutorials. It's really a boo-boo lol, the pipelines I found online kind of treating cellphonedb as an executable file, former version maybe. If it's possible I hope you can deleted this issue for this is also kind of misleading&useless information for those who really can't install cellphonedb.