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