1. Python2和Python3共存安装
Linux系统自带python版本为 2.7.5，CNVkit推荐使用python3，因此，在Linux上安装Python 3.9.2 版本
# Linux联网测试
ping www.baidu.com
PING www.wshifen.com (103.235.46.39) 56(84) bytes of data.
64 bytes from 103.235.46.39 (103.235.46.39): icmp_seq=1 ttl=55 time=249 ms
64 bytes from 103.235.46.39 (103.235.46.39): icmp_seq=2 ttl=55 time=249 ms
64 bytes from 103.235.46.39 (103.235.46.39): icmp_seq=3 ttl=55 time=249 ms
64 bytes from 103.235.46.39 (103.235.46.39): icmp_seq=4 ttl=55 time=249 ms
# 下载和安装Python
wget -c https://www.python.org/ftp/python/3.9.4/Python-3.9.4.tar.xz
tar -Jxvf Python-3.9.4.tar.xz
cd Python-3.9.4
# 配置python3安装路径;python2路径为/usr/bin/python2
./configure prefix=/usr/local/python3
# 编译安装python
make && make install
2. CNVKit安装
# CNVkit安装方法1
wget https://github.com/etal/cnvkit/archive/v0.9.7.zip
unzip v0.9.7.zip
cd cnvkit-0.9.7/
# CNVkit安装方法2
git clone https://github.com/etal/cnvkit
cd cnvkit/
/usr/local/python3/bin/pip3 install -e .
# 测试安装是否成功
/usr/local/python3/bin/python3 /opt/software/cnvkit-0.9.7/cnvkit.py -h
/usr/local/python3/bin/python3 /opt/software/cnvkit/cnvkit.py -h
# 报错
缺少pandas.png
3. 安装pandas库
/usr/local/python3/bin/pip3 install pandas
# 报错：pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.
缺少ssl.png
3. 1 确认缺少ssl模块错误：
在python shell import ssl同样提示找不到ssl模块
证实缺少ssl.png
3.2 解决缺少ssl模块问题：
使用rpm -aq|grep openssl命令查询openssl是否正确安装。发现缺少openssl-devel包
缺少level包.png
# 安装openssl-devel包
yum install -y openssl-devel
openssl-devel 包安装成功.png
3.3 测试问题是否解决
# 重新编译安装python
cd /opt/software/Python-3.9.2
make clean
# 配置安装路径
./configure prefix=/usr/local/python3
# 编译安装python
make && make install
# 重新安装pandas
/usr/local/python3/bin/pip3 install pandas
# pandas安装成功
/usr/local/python3/bin/pip3 list
pandas安装成功.png
#在python shell中 import ssl同样找到ssl模块
ssl 问题解决.png
4. 安装Bio库
# 成功安装pandas之后，测试CNVkit是否能正常运行，
/usr/local/python3/bin/python3 /opt/software/cnvkit-0.9.7/cnvkit.py -h
# 报错：ModuleNotFoundError: No module named 'Bio'
Bio包报错.png
4.1 解决缺少Bio库问题（此类报错解决原则缺什么补什么）：
# python安装Bio包
/usr/local/python3/bin/pip3 install Bio
# 仍然报错：ModuleNotFoundError: No module named 'Bio'
4.2 继续解决缺少Bio包问题：发现Bio库的安装并不是pip install bio，而是biopython
# 安装biopython
/usr/local/python3/bin/pip3 install biopython
# 还是报错：ModuleNotFoundError: No module named '_ctypes'
_ctypes 报错_version.png
# 搜索分析原因需要安装libffi-devel（参考：https://www.jianshu.com/p/b1f575c45e10）
yum install libffi-devel -y
# 重新编译安装python
cd /opt/software/Python-3.9.2
make clean
# 配置安装路径
./configure prefix=/usr/local/python3
# 编译安装python
make && make install
# 重新安装 biopython
/usr/local/python3/bin/pip3 install biopython
# biopython安装成功
biopython 安装成功.png
5. 安装pysam、scipy、ReportLab、pyfaidx和pomegranate库
# 成功安装biopython之后，测试CNVkit是否能正常运行，
/usr/local/python3/bin/python3 /opt/software/cnvkit-0.9.7/cnvkit.py -h
# 相同报错持续出现，不断安装即可：ModuleNotFoundError: No module named 'pysam' ；ModuleNotFoundError: No module named 'scipy'等等，不再复制了。
pysam缺少.png
缺少scipy.png
缺少ReportLab.png
缺少pyfaidx.png
缺少pomegranate.png
# 解决办法相同
#[图片上传中...(pysam安装成功.png-48740c-1616666692869-0)]
/usr/local/python3/bin/pip3 install pysam
/usr/local/python3/bin/pip3 install scipy
/usr/local/python3/bin/pip3 install ReportLab
/usr/local/python3/bin/pip3 install pyfaidx
/usr/local/python3/bin/pip3 install pomegranate
pysam安装成功.png
成功安装scipy.png
ReportLab安装成功.png
成功安装pyfaidx.png
pomegranate安装成功.png
6. 确认CNVkit安装成功
CNVkit 安装成功.png
7. 安装需要的 R依赖包，不安装的话CNVkit运行无法生成 .cns .pdf .png文件
# 安装 R软件
yum install R
# 加载需要的R包
> install.packages("BiocManager")
> library(BiocManager)
> BiocManager::install("DNAcopy")
> q()
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