How can I use scanpy_scripts? - Githubissues

ebi-gene-expression-group / scanpy-scripts

Scripts for using scanpy

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How can I use scanpy_scripts? #118

Open cooperist opened 1 year ago

cooperist commented 1 year ago

I have already installed it, but it always shows"ModuleNotFoundError: No module named 'scanpy_scripts'," how can I solve it?

cooperist commented 1 year ago

These are the packages that I have installed. blas 1.0 mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free blosc 1.21.0 h19a0ad4_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main bzip2 1.0.6 0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free certifi 2022.9.24 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main cffi 1.15.1 py37h2bbff1b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main click 8.0.3 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main cycler 0.11.0 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main freetype 2.10.4 hd328e21_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main glpk 4.65 h2bbff1b_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main h5py 2.8.0 py37h3bdd7fb_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main hdf5 1.10.2 hac2f561_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main icc_rt 2022.1.0 h6049295_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main icu 58.2 ha925a31_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main igraph 0.9.8 h29cbd77_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge intel-openmp 2022.0.0 haa95532_3663 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main jpeg 9e h2bbff1b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main kiwisolver 1.4.2 py37hd77b12b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main leidenalg 0.8.10 py37ha2e4c6b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libblas 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libcblas 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libiconv 1.16 h2bbff1b_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main liblapack 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge liblapacke 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libpng 1.6.37 h2a8f88b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main libxml2 2.9.14 h0ad7f3c_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main llvmlite 0.38.0 py37h23ce68f_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main loompy 3.0.6 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge louvain 0.7.0 py37ha2e4c6b_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge lz4-c 1.9.3 h2bbff1b_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main lzo 2.10 he774522_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main matplotlib 3.2.2 0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main matplotlib-base 3.2.2 py37h64f37c6_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main mkl 2020.2 256 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main mkl-service 2.3.0 py37h196d8e1_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main mpir 3.0.0 hec2e145_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main multicore-tsne 0.1_d4ff4aab py37h0a3528d_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge natsort 7.1.1 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main networkx 2.6.3 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main numba 0.55.1 py37hf11a4ad_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main numexpr 2.7.3 py37hcbcaa1e_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main numpy 1.18.1 py37h90d3380_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge numpy_groupies 0.9.19 pyhd8ed1ab_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge openssl 1.0.1k 1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free pandas 1.2.4 py37hf11a4ad_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main patsy 0.5.2 py37haa95532_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main pip 22.2.2 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main pycparser 2.21 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main pyparsing 3.0.9 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main pyqt 5.6.0 py37ha878b3d_6 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main pytables 3.4.4 py37he6f6034_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main python 3.7.0 hea74fb7_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main python-dateutil 2.8.2 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main python-igraph 0.9.10 py37hee3112d_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge python_abi 3.7 2_cp37m http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pytz 2022.1 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main qt 5.6.2 vc14h6f8c307_12 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main scanpy 1.4.3 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda scanpy-scripts 0.2.2 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda scikit-learn 0.20.3 py37h343c172_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main scipy 1.2.1 py37h29ff71c_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main seaborn 0.11.2 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main setuptools 63.4.1 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main sip 4.18.1 py37hd77b12b_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main six 1.16.0 pyhd3eb1b0_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main sqlite 3.39.3 h2bbff1b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main statsmodels 0.12.2 py37h2bbff1b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main suitesparse 5.4.0 h5d0cbe0_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge tbb 2021.6.0 h59b6b97_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main texttable 1.6.4 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main tornado 6.2 py37h2bbff1b_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main tqdm 4.62.3 pyhd3eb1b0_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main typing_extensions 4.3.0 py37haa95532_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main umap-learn 0.4.1 py37hc8dfbb8_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge vc 14.2 h21ff451_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main vs2015_runtime 14.27.29016 h5e58377_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main wheel 0.37.1 pyhd3eb1b0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main wincertstore 0.2 py37haa95532_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main zlib 1.2.12 h8cc25b3_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main zstd 1.5.2 h19a0ad4_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

cooperist commented 1 year ago

scanpy 1.4.3 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda scanpy-scripts 0.2.2 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda

pcm32 commented 1 year ago

Apologies, just saw this:

Setup bioconda as per usage here: https://bioconda.github.io/
create a conda env
inside that (conda activate ): mamba install scanpy-scripts
Run one of the commands, for instance read 10x:

(scanpy-scripts@1.1.6) :~ pcm32$ scanpy-cli read -x ~/10x_example_files/ /tmp/test.h5ad

in my case ~/10x_example_files/ contains matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz

(scanpy-scripts@1.1.6) :~ pcm32$ scanpy-cli --help

will show you potential commands. You can call --help again on top of commands.