velocyto的正确安装方法

如果你已经尝试了100种错误方法,恭喜你,找到家了。这个是99.9%能保证成功的安装方式。如果你第一篇就看到这个,更加恭喜你,你少走了一万里弯路!

总览

mamba create -n pyvelo
conda activate pyvelo
mamba install python
mamba install numpy scipy cython numba matplotlib scikit-learn h5py click
mamba install pysam
pip install velocyto

具体来看

1.首先创建一个环境 并安装python

(base) rstudio   ~
$ mamba create -n pyvelo

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

mamba (0.13.0) supported by @QuantStack

GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: []

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate pyvelo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) rstudio   ~
$ conda activate pyvelo
(pyvelo) rstudio   ~
$ mamba install python

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

mamba (0.13.0) supported by @QuantStack

GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['python']

pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
bioconda/linux-64        [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
conda-forge/noarch       [====================] (00m:01s) Done
conda-forge/linux-64     [====================] (00m:04s) Done
Transaction

Prefix: /home/rstudio/miniconda3/envs/pyvelo

Updating specs:

- python

Package             Version  Build           Channel                    Size
────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────

_libgcc_mutex           0.1  conda_forge     conda-forge/linux-64     Cached
  _openmp_mutex           4.5  1_gnu           conda-forge/linux-64     Cached
  ca-certificates   2021.5.30  ha878542_0      conda-forge/linux-64     Cached
  certifi           2021.5.30  py39hf3d152e_0  conda-forge/linux-64     Cached
  ld_impl_linux-64     2.35.1  hea4e1c9_2      conda-forge/linux-64     Cached
  libffi                  3.3  h58526e2_2      conda-forge/linux-64     Cached
  libgcc-ng             9.3.0  h2828fa1_19     conda-forge/linux-64     Cached
  libgomp               9.3.0  h2828fa1_19     conda-forge/linux-64     Cached
  libstdcxx-ng          9.3.0  h6de172a_19     conda-forge/linux-64     Cached
  ncurses                 6.2  h58526e2_4      conda-forge/linux-64     Cached
  openssl              1.1.1k  h7f98852_0      conda-forge/linux-64     Cached
  pip                  21.1.2  pyhd8ed1ab_0    conda-forge/noarch       Cached
  python                3.9.5  h12debd9_4      pkgs/main/linux-64       Cached
  python_abi              3.9  1_cp39          conda-forge/linux-64     Cached
  readline                8.1  h46c0cb4_0      conda-forge/linux-64     Cached
  setuptools           52.0.0  py39h06a4308_0  pkgs/main/linux-64       Cached
  sqlite               3.35.5  h74cdb3f_0      conda-forge/linux-64     Cached
  tk                   8.6.10  hed695b0_1      conda-forge/linux-64     Cached
  tzdata                2021a  he74cb21_0      conda-forge/noarch       Cached
  wheel                0.36.2  pyhd3deb0d_0    conda-forge/noarch       Cached
  xz                    5.2.5  h516909a_1      conda-forge/linux-64     Cached
  zlib                 1.2.11  h516909a_1010   conda-forge/linux-64     Cached

Summary:

Install: 22 packages

Total download: 0  B

────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(pyvelo) rstudio   ~
$ python
Python 3.9.5 (default, Jun  4 2021, 12:28:51) 
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> exit 
Use exit() or Ctrl-D (i.e. EOF) to exit
>>> exit()
(pyvelo) rstudio   ~

2.安装依赖包

$ mamba install numpy scipy cython numba matplotlib scikit-learn h5py click

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

mamba (0.13.0) supported by @QuantStack

GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['numpy', 'scipy', 'cython', 'numba', 'matplotlib', 'scikit-learn', 'h5py', 'click']

conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
bioconda/linux-64        Using cache
bioconda/noarch          Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
Transaction

Prefix: /home/rstudio/miniconda3/envs/pyvelo

Updating specs:

- numpy
   - scipy
   - cython
   - numba
   - matplotlib
   - scikit-learn
   - h5py
   - click

Package                Version  Build                   Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────

alsa-lib                 1.2.3  h516909a_0              conda-forge/linux-64     560 KB
  c-ares                  1.17.1  h7f98852_1              conda-forge/linux-64     Cached
  cached-property          1.5.2  hd8ed1ab_1              conda-forge/noarch         4 KB
  cached_property          1.5.2  pyha770c72_1            conda-forge/noarch        11 KB
  click                    8.0.1  py39hf3d152e_0          conda-forge/linux-64     146 KB
  cycler                  0.10.0  py_2                    conda-forge/noarch         9 KB
  cython                 0.29.23  py39he80948d_0          conda-forge/linux-64       2 MB
  dbus                   1.13.18  hb2f20db_0              pkgs/main/linux-64       504 KB
  expat                    2.4.1  h9c3ff4c_0              conda-forge/linux-64     Cached
  fontconfig              2.13.1  hba837de_1005           conda-forge/linux-64     Cached
  freetype                2.10.4  h0708190_1              conda-forge/linux-64     Cached
  gettext                 0.21.0  hf68c758_0              pkgs/main/linux-64       Cached
  glib                    2.68.2  h9c3ff4c_2              conda-forge/linux-64     450 KB
  glib-tools              2.68.2  h9c3ff4c_2              conda-forge/linux-64      86 KB
  gst-plugins-base        1.18.4  hf529b03_2              conda-forge/linux-64       3 MB
  gstreamer               1.18.4  h76c114f_2              conda-forge/linux-64       2 MB
  h5py                     3.2.1  nompi_py39h98ba4bc_100  conda-forge/linux-64       1 MB
  hdf5                    1.10.6  nompi_h6a2412b_1114     conda-forge/linux-64       3 MB
  icu                       68.1  h58526e2_0              conda-forge/linux-64     Cached
  joblib                   1.0.1  pyhd8ed1ab_0            conda-forge/noarch       206 KB
  jpeg                        9d  h516909a_0              conda-forge/linux-64     Cached
  kiwisolver               1.3.1  py39h1a9c180_1          conda-forge/linux-64      80 KB
  krb5                    1.19.1  hcc1bbae_0              conda-forge/linux-64     Cached
  lcms2                     2.12  hddcbb42_0              conda-forge/linux-64     443 KB
  libblas                  3.9.0  9_openblas              conda-forge/linux-64     Cached
  libcblas                 3.9.0  9_openblas              conda-forge/linux-64     Cached
  libclang                11.1.0  default_ha53f305_1      conda-forge/linux-64      19 MB
  libcurl                 7.77.0  h2574ce0_0              conda-forge/linux-64     Cached
  libedit           3.1.20210216  h27cfd23_1              pkgs/main/linux-64       Cached
  libev                     4.33  h516909a_1              conda-forge/linux-64     Cached
  libevent                2.1.10  hcdb4288_3              conda-forge/linux-64       1 MB
  libgfortran-ng           9.3.0  hff62375_19             conda-forge/linux-64     Cached
  libgfortran5             9.3.0  hff62375_19             conda-forge/linux-64     Cached
  libglib                 2.68.2  h3e27bee_2              conda-forge/linux-64     Cached
  libiconv                  1.16  h516909a_0              conda-forge/linux-64     Cached
  liblapack                3.9.0  9_openblas              conda-forge/linux-64     Cached
  libllvm10               10.0.1  he513fc3_3              conda-forge/linux-64      26 MB
  libllvm11               11.1.0  hf817b99_2              conda-forge/linux-64      29 MB
  libnghttp2              1.43.0  h812cca2_0              conda-forge/linux-64     Cached
  libogg                   1.3.5  h27cfd23_1              pkgs/main/linux-64       199 KB
  libopenblas             0.3.15  pthreads_h8fe5266_1     conda-forge/linux-64     Cached
  libopus                  1.3.1  h7f98852_1              conda-forge/linux-64     255 KB
  libpng                  1.6.37  hed695b0_2              conda-forge/linux-64     Cached
  libpq                     13.3  hd57d9b9_0              conda-forge/linux-64       3 MB
  libssh2                  1.9.0  ha56f1ee_6              conda-forge/linux-64     Cached
  libtiff                  4.2.0  hbd63e13_2              conda-forge/linux-64     639 KB
  libuuid                 2.32.1  h14c3975_1000           conda-forge/linux-64     Cached
  libvorbis                1.3.7  he1b5a44_0              conda-forge/linux-64     287 KB
  libwebp-base             1.2.0  h7f98852_2              conda-forge/linux-64     Cached
  libxcb                    1.14  h7b6447c_0              pkgs/main/linux-64       Cached
  libxkbcommon             1.0.3  he3ba5ed_0              conda-forge/linux-64     581 KB
  libxml2                 2.9.12  h72842e0_0              conda-forge/linux-64     Cached
  llvmlite                0.36.0  py39h1bbdace_0          conda-forge/linux-64       3 MB
  lz4-c                    1.9.3  h9c3ff4c_0              conda-forge/linux-64     Cached
  matplotlib               3.4.2  py39hf3d152e_0          conda-forge/linux-64       7 KB
  matplotlib-base          3.4.2  py39h2fa2bec_0          conda-forge/linux-64       7 MB
  mysql-common            8.0.23  ha770c72_2              conda-forge/linux-64       2 MB
  mysql-libs              8.0.23  h935591d_2              conda-forge/linux-64       2 MB
  nspr                      4.30  h9c3ff4c_0              conda-forge/linux-64     233 KB
  nss                       3.66  hb5efdd6_0              conda-forge/linux-64       2 MB
  numba                   0.53.1  py39h4292f66_0          conda-forge/linux-64       4 MB
  numpy                   1.20.3  py39hdbf815f_1          conda-forge/linux-64     Cached
  olefile                   0.46  pyh9f0ad1d_1            conda-forge/noarch        32 KB
  openjpeg                 2.4.0  hb52868f_1              conda-forge/linux-64     444 KB
  pcre                      8.44  he1b5a44_0              conda-forge/linux-64     Cached
  pillow                   8.2.0  py39hf95b381_1          conda-forge/linux-64     690 KB
  pyparsing                2.4.7  pyh9f0ad1d_0            conda-forge/noarch        60 KB
  pyqt                    5.12.3  py39hf3d152e_7          conda-forge/linux-64      21 KB
  pyqt-impl               5.12.3  py39h0fcd23e_7          conda-forge/linux-64       6 MB
  pyqt5-sip              4.19.18  py39he80948d_7          conda-forge/linux-64     310 KB
  pyqtchart                 5.12  py39h0fcd23e_7          conda-forge/linux-64     253 KB
  pyqtwebengine           5.12.1  py39h0fcd23e_7          conda-forge/linux-64     174 KB
  python-dateutil          2.8.1  py_0                    conda-forge/noarch       220 KB
  qt                      5.12.9  hda022c4_4              conda-forge/linux-64     100 MB
  scikit-learn            0.24.2  py39h4dfa638_0          conda-forge/linux-64       8 MB
  scipy                    1.6.3  py39hee8e79c_0          conda-forge/linux-64      21 MB
  six                     1.16.0  pyh6c4a22f_0            conda-forge/noarch        14 KB
  threadpoolctl            2.1.0  pyh5ca1d4c_0            conda-forge/noarch        15 KB
  tornado                    6.1  py39h3811e60_1          conda-forge/linux-64     646 KB
  zstd                     1.4.9  ha95c52a_0              conda-forge/linux-64     431 KB

Summary:

Install: 80 packages

Total download: 250 MB

───────────────────────────────────────────────────────────────────────────────────────────

Finished click                                (00m:00s)             146 KB    914 KB/s
Finished kiwisolver                           (00m:00s)              80 KB    447 KB/s
Finished pyqt5-sip                            (00m:00s)             310 KB      2 MB/s
Finished tornado                              (00m:00s)             646 KB      3 MB/s
Finished libopus                              (00m:00s)             255 KB      1 MB/s
Finished cython                               (00m:00s)               2 MB     10 MB/s
Finished lcms2                                (00m:00s)             443 KB      2 MB/s
Finished mysql-libs                           (00m:00s)               2 MB      6 MB/s
Finished pyparsing                            (00m:00s)              60 KB    208 KB/s
Finished olefile                              (00m:00s)              32 KB    112 KB/s
Finished nss                                  (00m:00s)               2 MB      7 MB/s
Finished cached-property                      (00m:00s)               4 KB     13 KB/s
Finished h5py                                 (00m:00s)               1 MB      3 MB/s
Finished pillow                               (00m:00s)             690 KB      1 MB/s
Finished hdf5                                 (00m:01s)               3 MB      6 MB/s
Finished matplotlib-base                      (00m:01s)               7 MB     14 MB/s
Finished pyqt                                 (00m:01s)              21 KB     38 KB/s
Finished alsa-lib                             (00m:01s)             560 KB    878 KB/s
Finished pyqt-impl                            (00m:02s)               6 MB      9 MB/s
Finished libxkbcommon                         (00m:02s)             581 KB    808 KB/s
Finished cached_property                      (00m:02s)              11 KB     15 KB/s
Finished joblib                               (00m:02s)             206 KB    284 KB/s
Finished scipy                                (00m:05s)              21 MB     31 MB/s
Finished libpq                                (00m:04s)               3 MB      3 MB/s
Finished gstreamer                            (00m:05s)               2 MB      2 MB/s
Finished pyqtwebengine                        (00m:05s)             174 KB    185 KB/s
Finished libogg                               (00m:05s)             199 KB    184 KB/s
Finished llvmlite                             (00m:05s)               3 MB      3 MB/s
Finished threadpoolctl                        (00m:05s)              15 KB     13 KB/s
Finished cycler                               (00m:05s)               9 KB      8 KB/s
Finished glib-tools                           (00m:05s)              86 KB     69 KB/s
Finished libclang                             (00m:07s)              19 MB     16 MB/s
Finished libllvm11                            (00m:10s)              29 MB     23 MB/s
Finished libevent                             (00m:10s)               1 MB    781 KB/s
Finished mysql-common                         (00m:10s)               2 MB      1 MB/s
Finished python-dateutil                      (00m:10s)             220 KB    152 KB/s
Finished libtiff                              (00m:10s)             639 KB    432 KB/s
Finished pyqtchart                            (00m:10s)             253 KB    169 KB/s
Finished gst-plugins-base                     (00m:10s)               3 MB      2 MB/s
Finished zstd                                 (00m:10s)             431 KB    280 KB/s
Finished six                                  (00m:10s)              14 KB      9 KB/s
Finished dbus                                 (00m:10s)             504 KB    326 KB/s
Finished nspr                                 (00m:10s)             233 KB    149 KB/s
Finished libvorbis                            (00m:10s)             287 KB    181 KB/s
Finished glib                                 (00m:10s)             450 KB    281 KB/s
Finished libllvm10                            (00m:14s)              26 MB     17 MB/s
Finished openjpeg                             (00m:13s)             444 KB    263 KB/s
Finished numba                                (00m:14s)               4 MB      2 MB/s
Finished matplotlib                           (00m:13s)               7 KB      4 KB/s
Finished scikit-learn                         (00m:14s)               8 MB      4 MB/s
Finished qt                                   (00m:25s)             100 MB     35 MB/s
Downloading  [========================================================] (00m:27s) 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(pyvelo) rstudio   ~

3.再安装依赖包

$ mamba install pysam

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

mamba (0.13.0) supported by @QuantStack

GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['pysam']

conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
bioconda/linux-64        Using cache
bioconda/noarch          Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
Transaction

Prefix: /home/rstudio/miniconda3/envs/pyvelo

Updating specs:

- pysam

Package      Version  Build           Channel                    Size
─────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────

bzip2          1.0.8  h7f98852_4      conda-forge/linux-64     Cached
  libdeflate       1.7  h7f98852_5      conda-forge/linux-64     Cached
  pysam       0.16.0.1  py39h051187c_3  bioconda/linux-64          3 MB

Summary:

Install: 3 packages

Total download: 3 MB

─────────────────────────────────────────────────────────────────────────

Finished pysam                                (00m:00s)               3 MB     11 MB/s
Downloading  [========================================================] (00m:00s) 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(pyvelo) rstudio   ~
###错误尝试
$ mamba install velocyto

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

mamba (0.13.0) supported by @QuantStack

GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['velocyto']

conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
bioconda/linux-64        Using cache
bioconda/noarch          Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
Encountered problems while solving:
  - nothing provides requested velocyto

(pyvelo) rstudio   ~

4.正确安装velocyto

$ pip install velocyto
Collecting velocyto
  Downloading velocyto-0.17.17.tar.gz (198 kB)
     |################################| 198 kB 18.7 MB/s 
Requirement already satisfied: numpy in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (1.20.3)
Requirement already satisfied: scipy in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (1.6.3)
Requirement already satisfied: cython in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (0.29.23)
Requirement already satisfied: numba in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (0.53.1)
Requirement already satisfied: matplotlib in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (3.4.2)
Requirement already satisfied: scikit-learn in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (0.24.2)
Requirement already satisfied: h5py in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (3.2.1)
Collecting loompy
  Downloading loompy-3.0.6.tar.gz (41 kB)
     |################################| 41 kB 376 kB/s 
Requirement already satisfied: pysam in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (0.16.0.1)
Requirement already satisfied: Click in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from velocyto) (8.0.1)
Collecting pandas
  Downloading pandas-1.2.4-cp39-cp39-manylinux1_x86_64.whl (9.7 MB)
     |################################| 9.7 MB 41.9 MB/s 
Requirement already satisfied: setuptools in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from loompy->velocyto) (52.0.0.post20210125)
Collecting numpy-groupies
  Downloading numpy_groupies-0.9.13.tar.gz (109 kB)
     |################################| 109 kB 44.7 MB/s 
Requirement already satisfied: pillow>=6.2.0 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (8.2.0)
Requirement already satisfied: python-dateutil>=2.7 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (2.8.1)
Requirement already satisfied: pyparsing>=2.2.1 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (2.4.7)
Requirement already satisfied: cycler>=0.10 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (1.3.1)
Requirement already satisfied: six in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from cycler>=0.10->matplotlib->velocyto) (1.16.0)
Requirement already satisfied: llvmlite<0.37,>=0.36.0rc1 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from numba->velocyto) (0.36.0)
Collecting pytz>=2017.3
  Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB)
     |################################| 510 kB 31.8 MB/s 
Requirement already satisfied: threadpoolctl>=2.0.0 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from scikit-learn->velocyto) (2.1.0)
Requirement already satisfied: joblib>=0.11 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from scikit-learn->velocyto) (1.0.1)
Building wheels for collected packages: velocyto, loompy, numpy-groupies
  Building wheel for velocyto (setup.py) ... done
  Created wheel for velocyto: filename=velocyto-0.17.17-cp39-cp39-linux_x86_64.whl size=170974 sha256=cecd6c39bf17f97bff00d5656ffbbe1a357c267f0e5b8c7ea3ef481fba03108c
  Stored in directory: /home/rstudio/.cache/pip/wheels/f5/d4/c7/f081e3c830f30e77bc4af9915e07e4f61e715f1af623fab721
  Building wheel for loompy (setup.py) ... done
  Created wheel for loompy: filename=loompy-3.0.6-py3-none-any.whl size=47895 sha256=c8d95964536b14bcf11c2e91a581dde4e91673e87d3e8fec40d6a01d23b320c0
  Stored in directory: /home/rstudio/.cache/pip/wheels/f0/41/f4/02a35a0f853fd71e2a3979131cc803922860e7db126042bc14
  Building wheel for numpy-groupies (setup.py) ... done
  Created wheel for numpy-groupies: filename=numpy_groupies-0.9.13-py3-none-any.whl size=24068 sha256=680874f1ecced40e27c4bbd47011d188e4d21bd7beb0c90f68e4a2ae07ed6ecb
  Stored in directory: /home/rstudio/.cache/pip/wheels/a7/55/f6/7ee852d35817ee56ec3dc4abf145e414951092dcc7458a0860
Successfully built velocyto loompy numpy-groupies
Installing collected packages: pytz, numpy-groupies, pandas, loompy, velocyto
Successfully installed loompy-3.0.6 numpy-groupies-0.9.13 pandas-1.2.4 pytz-2021.1 velocyto-0.17.17
(pyvelo) rstudio   ~

5.查看帮助文档 验证安装成功

$ velocyto --help
Unable to revert mtime: /usr/share/fonts/cMap
Unable to revert mtime: /usr/share/fonts/cmap/adobe-cns1
Unable to revert mtime: /usr/share/fonts/cmap/adobe-gb1
Unable to revert mtime: /usr/share/fonts/cmap/adobe-japan1
Unable to revert mtime: /usr/share/fonts/cmap/adobe-japan2
Unable to revert mtime: /usr/share/fonts/cmap/adobe-korea1
Unable to revert mtime: /usr/share/fonts/eot/font-awesome
Unable to revert mtime: /usr/share/fonts/svg/font-awesome
Usage: velocyto [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  run            Runs the velocity analysis outputting a loom file
  run10x         Runs the velocity analysis for a Chromium Sample
  run-dropest    Runs the velocity analysis on DropEst preprocessed data
  run-smartseq2  Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)
  tools          helper tools for velocyto
(pyvelo) rstudio   ~

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