linux下安装RSeQC避坑指南（二）

最新推荐文章于 2023-01-22 09:41:06 发布

WLDLSW

最新推荐文章于 2023-01-22 09:41:06 发布

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本文链接：https://blog.csdn.net/WLDLSW/article/details/128661424

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linux下安装RSeQC避坑指南（二）

https://editor.csdn.net/md/?articleId=127723427
对于上篇写个后续👆，
总之非常悲惨，因为RSeQC是个python包，所以就算我在同一个环境中，当我安装其他python写的包时所需依赖包就很容易冲突……
在这我列下安装RSeQC所需要的所有python包，以便日后冲突有据可循
照旧，我仍然是python2安装的

cython>=0.17
numpy
pysam
bx-python

#安装numpy附带安装了以下依赖包
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.9.0              |16_linux64_openblas          13 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libcblas-3.9.0             |16_linux64_openblas          13 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libgfortran-ng-12.2.0      |      h69a702a_19          22 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libgfortran5-12.2.0        |      h337968e_19         1.8 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    liblapack-3.9.0            |16_linux64_openblas          13 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    numpy-1.15.4               |py27h8b7e671_1002         4.1 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:         5.9 MB

The following NEW packages will be INSTALLED:

  libblas            anaconda/cloud/conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas None
  libcblas           anaconda/cloud/conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas None
  libgfortran-ng     anaconda/cloud/conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19 None
  libgfortran5       anaconda/cloud/conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19 None
  liblapack          anaconda/cloud/conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas None
  libopenblas        anaconda/cloud/conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3 None
  numpy              anaconda/cloud/conda-forge/linux-64::numpy-1.15.4-py27h8b7e671_1002 None

#安装pysam
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    curl-7.87.0                |       h6312ad2_0          86 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    krb5-1.20.1                |       hf9c8cef_0         1.3 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libcurl-7.87.0             |       h6312ad2_0         339 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libnghttp2-1.51.0          |       hdcd2b5c_0         608 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pysam-0.15.3               |   py27hda2845c_1         2.6 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    ------------------------------------------------------------
                                           Total:         4.9 MB

The following NEW packages will be INSTALLED:

  bzip2              anaconda/cloud/conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 None
  c-ares             anaconda/cloud/conda-forge/linux-64::c-ares-1.18.1-h7f98852_0 None
  curl               anaconda/cloud/conda-forge/linux-64::curl-7.87.0-h6312ad2_0 None
  keyutils           anaconda/cloud/conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 None
  krb5               anaconda/cloud/conda-forge/linux-64::krb5-1.20.1-hf9c8cef_0 None
  libcurl            anaconda/cloud/conda-forge/linux-64::libcurl-7.87.0-h6312ad2_0 None
  libdeflate         anaconda/cloud/bioconda/linux-64::libdeflate-1.0-h14c3975_1 None
  libedit            anaconda/cloud/conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 None
  libev              anaconda/cloud/conda-forge/linux-64::libev-4.33-h516909a_1 None
  libnghttp2         anaconda/cloud/conda-forge/linux-64::libnghttp2-1.51.0-hdcd2b5c_0 None
  libssh2            anaconda/cloud/conda-forge/linux-64::libssh2-1.10.0-haa6b8db_3 None
  pysam              anaconda/cloud/bioconda/linux-64::pysam-0.15.3-py27hda2845c_1 None
  xz                 anaconda/cloud/conda-forge/linux-64::xz-5.2.6-h166bdaf_0 None

#安装bx-python
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bx-python-0.8.9            |   py27h54ae540_2        1021 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    certifi-2019.11.28         |   py27h8c360ce_1         149 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    lzo-2.10                   |    h516909a_1000         314 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    python-lzo-1.12            |py27h42e1302_1001          18 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:         1.5 MB

The following NEW packages will be INSTALLED:

  bx-python          anaconda/cloud/bioconda/linux-64::bx-python-0.8.9-py27h54ae540_2 None
  lzo                anaconda/cloud/conda-forge/linux-64::lzo-2.10-h516909a_1000 None
  python-lzo         anaconda/cloud/conda-forge/linux-64::python-lzo-1.12-py27h42e1302_1001 None
  six                anaconda/cloud/conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 None

The following packages will be UPDATED:

  certifi                                  2016.9.26-py27_0 --> 2019.11.28-py27h8c360ce_1 None

#最后 pip install RSeQC

Collecting RSeQC
  Using cached RSeQC-2.6.6-py2-none-any.whl (129 kB)
Collecting cython>=0.17
  Using cached Cython-0.29.33-cp27-cp27mu-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.9 MB)
Requirement already satisfied: numpy in ./miniconda3/envs/RNASEQ1/lib/python2.7/site-packages (from RSeQC) (1.15.4)
Requirement already satisfied: pysam in ./miniconda3/envs/RNASEQ1/lib/python2.7/site-packages (from RSeQC) (0.15.3)
Requirement already satisfied: bx-python in ./miniconda3/envs/RNASEQ1/lib/python2.7/site-packages (from RSeQC) (0.8.9)
Requirement already satisfied: six>=1.13.0 in ./miniconda3/envs/RNASEQ1/lib/python2.7/site-packages (from bx-python->RSeQC) (1.16.0)
Installing collected packages: cython, RSeQC
Successfully installed RSeQC-2.6.6 cython-0.29.33