How can I use scanpy_scripts?

[cooperist]

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

[cooperist]

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]

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]

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:

([email protected]) :~ 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

([email protected]) :~ pcm32$ scanpy-cli --help

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