linux中python安装scanpy安装进行单细胞分析scrnaseq-CSDN博客

本文链接：https://blog.csdn.net/qq_52813185/article/details/128422965

Linux安装conda Ubuntu安装conda Linux安装百度云 Ubuntu安装百度云服务器安装百度云 Linux上传到百度云 Linux上传文件到百度云 Linux从百度云下载_YoungLeelight的博客-CSDN博客

前置内容：在linux 中安装conda

$ nohup  wget -c https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh &

1.建立rna环境

2.conda install scanpy 安装scanpy

conda install -c conda-forge scanpy python-igraph leidenalg

查看 list 发现scanpy安装好了

$ conda list
# packages in environment at /home/st8/ssd2/tree119/miniconda3/envs/rna:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
anndata                   0.7.8            py37h89c1867_1    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
blas                      1.0                         mkl    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
blosc                     1.21.0               h4ff587b_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
bottleneck                1.3.5            py37h7deecbd_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
brotlipy                  0.7.0           py37h27cfd23_1003    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
bz2file                   0.98             py37h06a4308_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
bzip2                     1.0.8                h7b6447c_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
c-ares                    1.18.1               h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ca-certificates           2022.10.11           h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
certifi                   2022.12.7        py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
cffi                      1.15.1           py37h5eee18b_2    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
charset-normalizer        2.0.4              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
click                     8.0.4            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
colorama                  0.4.5            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
coloredlogs               15.0.1           py37h06a4308_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
colormath                 3.0.0                      py_2    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
commonmark                0.9.1              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
cryptography              38.0.1           py37h9ce1e76_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
curl                      7.86.0               h5eee18b_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
cutadapt                  1.18             py37h14c3975_1    bioconda
cycler                    0.11.0             pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dataclasses               0.8                pyh6d0b6a4_7    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dbus                      1.13.18              hb2f20db_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
decorator                 4.4.0                    py37_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dunamai                   1.15.0             pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
expat                     2.4.9                h6a678d5_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fastqc                    0.11.9               hdfd78af_1    bioconda
flit-core                 3.6.0              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
font-ttf-dejavu-sans-mono 2.37                 hd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fontconfig                2.14.1               hef1e5e3_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
freetype                  2.12.1               h4a9f257_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
future                    0.18.2                   py37_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
gdbm                      1.18                 hd4cb3f1_4    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
get_version               3.5.4              pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
gettext                   0.21.0               hf68c758_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
git                       2.34.1          pl5262hc120c5b_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
glib                      2.69.1               he621ea3_2    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
h5py                      2.10.0           py37h7918eee_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
hdf5                      1.10.4               hb1b8bf9_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
hisat2                    2.2.1                h87f3376_4    bioconda
htslib                    1.16                 h6bc39ce_0    bioconda
humanfriendly             10.0             py37h06a4308_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
icu                       58.2                 he6710b0_3    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
idna                      3.4              py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
importlib-metadata        4.11.3           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
importlib_metadata        4.11.3               hd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
intel-openmp              2021.4.0          h06a4308_3561    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
jemalloc                  5.2.1                h2531618_5    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
jinja2                    3.1.2            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
joblib                    1.1.1            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
kiwisolver                1.4.2            py37h295c915_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
krb5                      1.19.2               hac12032_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ld_impl_linux-64          2.38                 h1181459_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
legacy-api-wrap           1.2                        py_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libboost                  1.73.0              h28710b8_12    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libcurl                   7.86.0               h91b91d3_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libdeflate                1.13                 h166bdaf_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libedit                   3.1.20210910         h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libev                     4.33                 h7f8727e_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libffi                    3.4.2                h6a678d5_6    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libgcc-ng                 12.2.0              h65d4601_19    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            7.5.0               ha8ba4b0_17    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libgfortran4              7.5.0               ha8ba4b0_17    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libllvm10                 10.0.1               hbcb73fb_5    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libnghttp2                1.46.0               hce63b2e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libpng                    1.6.37               hbc83047_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libssh2                   1.10.0               h8f2d780_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libstdcxx-ng              11.2.0               h1234567_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxcb                    1.15                 h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxml2                   2.9.14               h74e7548_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libzlib                   1.2.13               h166bdaf_4    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
llvm-openmp               14.0.6               h9e868ea_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
llvmlite                  0.36.0           py37h612dafd_4    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
lz4-c                     1.9.3                h295c915_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
lzo                       2.10                 h7b6447c_2    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
lzstring                  1.0.4                   py_1001    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
markdown                  3.3.4            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
markupsafe                2.1.1            py37h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
matplotlib-base           3.1.3            py37hef1b27d_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
mkl                       2021.4.0           h06a4308_640    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
mkl-service               2.4.0            py37h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
mkl_fft                   1.3.1            py37hd3c417c_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
mkl_random                1.2.2            py37h51133e4_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
mock                      4.0.3              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
multiqc                   1.13               pyhdfd78af_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
natsort                   7.1.1              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ncurses                   6.3                  h5eee18b_3    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
networkx                  2.5.1              pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
numba                     0.53.1           py37ha9443f7_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
numexpr                   2.8.4            py37he184ba9_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
numpy                     1.21.5           py37h6c91a56_3    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
numpy-base                1.21.5           py37ha15fc14_3    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
openjdk                   11.0.13              h87a67e3_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
openssl                   1.1.1s               h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
packaging                 22.0             py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pandas                    1.3.5            py37h8c16a72_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
patsy                     0.5.2            py37h06a4308_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pcre                      8.45                 h295c915_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pcre2                     10.37                he7ceb23_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
perl                      5.34.0               h5eee18b_2    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pigz                      2.6                  h27cfd23_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pip                       22.2.2           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pycparser                 2.21               pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pygments                  2.11.2             pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pynndescent               0.5.4              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pyopenssl                 22.0.0             pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pyparsing                 3.0.9            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pysocks                   1.7.1                    py37_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pytables                  3.6.1            py37h71ec239_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
python                    3.7.15               h7a1cb2a_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
python-dateutil           2.8.2              pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
python_abi                3.7                     2_cp37m    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
pytz                      2022.7           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pyyaml                    6.0              py37h7f8727e_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
readline                  8.2                  h5eee18b_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
requests                  2.28.1           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
rich                      12.5.1           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
rich-click                1.5.2              pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
salmon                    0.13.1               h86b0361_0    bioconda
samtools                  1.16.1               h6899075_1    bioconda
scanpy                    1.8.2              pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
scikit-learn              1.0.2            py37h51133e4_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
scipy                     1.7.3            py37hc147768_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
seaborn                   0.12.1           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
setuptools                65.5.0           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
simplejson                3.17.6           py37h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
sinfo                     0.3.1                      py_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
six                       1.16.0             pyhd3eb1b0_1    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
spectra                   0.0.11                     py_1    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
sqlite                    3.40.0               h5082296_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
statsmodels               0.13.2           py37h7f8727e_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
stdlib-list               0.8.0              pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
subread                   2.0.1                h7132678_2    bioconda
tbb                       2020.2               h4bd325d_4    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
threadpoolctl             2.2.0              pyh0d69192_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
tk                        8.6.12               h1ccaba5_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
tornado                   6.2              py37h5eee18b_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
tqdm                      4.64.1           py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
trim-galore               0.6.7                hdfd78af_0    bioconda
typing_extensions         4.4.0            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
umap-learn                0.5.3            py37h89c1867_0    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
urllib3                   1.26.12          py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
wheel                     0.37.1             pyhd3eb1b0_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
xopen                     0.7.3                      py_0    bioconda
xz                        5.2.8                h5eee18b_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
yaml                      0.2.5                h7b6447c_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
zipp                      3.8.0            py37h06a4308_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
zlib                      1.2.13               h166bdaf_4    https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.2                ha4553b6_0    https://mirrors.bfsu.edu.cn/anaconda/pkgs/main