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！
1.首先创建一个环境 并安装python
(base) rstudio ~
$ mamba create -n pyvelo
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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
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/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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
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|/
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██╔████╔██║███████║██╔████╔██║██████╔╝███████║
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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)
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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)
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Requirement already satisfied: pillow>=6.2.0 in ./miniconda3/envs/pyvelo/lib/python3.9/site-packages (from matplotlib->velocyto) (8.2.0)
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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)
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Collecting pytz>=2017.3
Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB)
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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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