编程，作为生物信息学的一个基础性技能，是任何一个生信工程师都无法绕开话题。也许有些人还在纠结 Perl 和 Python 到底应该学习哪一个，但作为目前最火最流行的编程语言 Python 还是非常值得尝试的。它不但可以进行文本处理，在统计、网站、游戏、爬虫、数据可视化等方面也有非常强大的应用，比起曾经的 Perl 真的强大和全面很多，且在学习曲线上比 Perl 更容易入手。不管从长远发展，还是短期需要，学会 Python，看懂 Perl (或者先学  Python，后学 Perl) 应该是每一个生信工程必备的基础技能之一。

工欲善其事，必先利其器。关于 Python 安装教程在网上一搜一大把，但总感觉不够全面，尤其对于中间出现的一些问题的解决方法不尽如人意。鉴于此，本文基于 CentOS Linux release 6.5 对 python-3.7.3 的源码编译安装进行了一下简单的总结，记录如下。

1. 安装环境

操作系统  ：CentOS Linux release 6.5 (x86_64)GCC 版本：4.8.5 20150623

2. 安装步骤

如果您拥有 root 权限，请执以下依赖安装：

yum install zlibyum install zlib-develyum install opensslyum install openssl-develyum install libffiyum install libffi-devel

如果您没有 root 权限，可以参考《手把手教你如何在 Linux 上源码安装最新版本 R》一文，手动一个个去解决以上的依赖。

2.1 ssl

python3 需要引用openssl模块，但是 CentOS 需要的 openssl 版本最低为 1.0.2，而 CentOS 默认的为 1.0.1（CentOS-6.x 通过yum源安装的 openssl 的最高版本是 1.0.1），所以需要手动更新 openssl。

# 下载wget http://www.openssl.org/source/openssl-1.1.1.tar.gz

# 解压缩tar -zxvf openssl-1.1.1.tar.gz

# 进入目录安装cd openssl-1.1.1

# 进行配置下，自定义./config --prefix=$HOME/soft-repos/openssl shared zlib

# 编译并安装make && make install

# 配置到用户环境变量，随处使用echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/soft-repos/openssl/lib" >> $HOME/.bashrc

# 是环境变量配置生效source $HOME/.bashrc

请注意：

1. openssl 编译（config）的时候必须要加上 shared 参数，否者源码安装 Python 即使添加了--with-openssl的自定义路径，依然会导致Could not build the ssl module!报错！

2. 从https://www.openssl.org/source/下载的源码 openssl-1.0.2s、openssl-1.0.2m，包括 CentOS-7.5 使用yum安装的最高版本的 openssl-1.0.2k 目前发现依然会导致Could not build the ssl module，建议从https://www.openssl.org/source/old/下载 1.1.1 的源码编译安装。

2.2 ctypes

在 CentOS 6.x 安装libffi-devel的时候出现以下问题：

$ yum install -y libffi-develLoaded plugins: product-id, refresh-packagekit, search-disabled-repos, security, subscription-managerThis system is not registered to Red Hat Subscription Management. You can use subscription-manager to register.Setting up Install Processcdrom                                                                                                                                         | 4.1 kB     00:00 ...No package libffi-devel available.Error: Nothing to do

可以使用下面的方法安装：

[root@log01 ~]# rpm -ivh http://mirror.centos.org/centos/6/os/x86_64/Packages/libffi-devel-3.0.5-3.2.el6.x86_64.rpmRetrieving http://mirror.centos.org/centos/6/os/x86_64/Packages/libffi-devel-3.0.5-3.2.el6.x86_64.rpmwarning: /var/tmp/rpm-tmp.V9ihbu: Header V3 RSA/SHA256 Signature, key ID c105b9de: NOKEYPreparing...                ########################################### [100%]   1:libffi-devel           ########################################### [100%][root@log01 ~]# rpm -qa|grep libffilibffi-3.0.5-3.2.el6.x86_64libffi-devel-3.0.5-3.2.el6.x86_64

源码方法安装如下：

$ wget ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz$ tar zvxf libffi-3.2.1.tar.gz$ ./configure --prefix=/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1$ make $ make install 

2.3 pygraphviz

$ /Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/pip3 install pygraphvizCollecting pygraphviz  Using cached https://files.pythonhosted.org/packages/7e/b1/d6d849ddaf6f11036f9980d433f383d4c13d1ebcfc3cd09bc845bda7e433/pygraphviz-1.5.zipInstalling collected packages: pygraphviz  Running setup.py install for pygraphviz ... error    Complete output from command /Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-_zdjdg0j/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-g0mz7lrq/install-record.txt --single-version-externally-managed --compile:    running install    Trying dpkg    Failed to find dpkg    Trying pkg-config    Package libcgraph was not found in the pkg-config search path.    Perhaps you should add the directory containing `libcgraph.pc'    to the PKG_CONFIG_PATH environment variable    No package 'libcgraph' found    Traceback (most recent call last):      File "<string>", line 1, in <module>      File "/tmp/pip-install-_zdjdg0j/pygraphviz/setup.py", line 93, in <module>        tests_require=['nose>=1.3.7', 'doctest-ignore-unicode>=0.1.2', 'mock>=2.0.0'],      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup        return distutils.core.setup(**attrs)      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/distutils/core.py", line 148, in setup        dist.run_commands()      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/distutils/dist.py", line 966, in run_commands        self.run_command(cmd)      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/distutils/dist.py", line 985, in run_command        cmd_obj.run()      File "/tmp/pip-install-_zdjdg0j/pygraphviz/setup_commands.py", line 44, in modified_run        self.include_path, self.library_path = get_graphviz_dirs()      File "/tmp/pip-install-_zdjdg0j/pygraphviz/setup_extra.py", line 162, in get_graphviz_dirs        include_dirs, library_dirs = _try_configure(include_dirs, library_dirs, _pkg_config)      File "/tmp/pip-install-_zdjdg0j/pygraphviz/setup_extra.py", line 117, in _try_configure        i, l = try_function()      File "/tmp/pip-install-_zdjdg0j/pygraphviz/setup_extra.py", line 72, in _pkg_config        output = S.check_output(['pkg-config', '--libs-only-L', 'libcgraph'])      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/subprocess.py", line 395, in check_output        **kwargs).stdout      File "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/subprocess.py", line 487, in run        output=stdout, stderr=stderr)    subprocess.CalledProcessError: Command '['pkg-config', '--libs-only-L', 'libcgraph']' returned non-zero exit status 1.

    ----------------------------------------Command "/Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-_zdjdg0j/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-g0mz7lrq/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-_zdjdg0j/pygraphviz/

参考：《Installation:fatal error: 'graphviz/cgraph.h' file not found》

$ wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz$ tar zvxf graphviz.tar.gz$ cd graphviz-2.40.1$ ./configure --prefix=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1$ make && make install

推荐把安装好的 graphviz 添加到环境变量，这样可以避免运行过程中出现："pygraphviz/graphviz_wrap.c:2987:29: fatal error: graphviz/cgraph.h: No such file or directory"  无法找到头文件的异常。

export PKG_CONFIG_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib/pkgconfig:$PKG_CONFIG_PATHexport LD_LIBRARY_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib:$LD_LIBRARY_PATHexport C_INCLUDE_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include:$C_INCLUDE_PATHexport CPLUS_INCLUDE_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include:$CPLUS_INCLUDE_PATH

如果 graphviz 添加到环境变量，pygraphviz的 python 包可以参考下面的方法安装：

$ /Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/pip3 install --global-option=build_ext --global-option="-I/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include" --global-option="-L/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib" pygraphviz/Bioinfo/Pipeline/SoftWare/Python-3.7.3/lib/python3.7/site-packages/pip/_internal/commands/install.py:207: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.  cmdoptions.check_install_build_global(options)Collecting pygraphviz  Using cached https://files.pythonhosted.org/packages/7e/b1/d6d849ddaf6f11036f9980d433f383d4c13d1ebcfc3cd09bc845bda7e433/pygraphviz-1.5.zipInstalling collected packages: pygraphviz  Running setup.py install for pygraphviz ... doneSuccessfully installed pygraphviz-1.5

2.4 编译安装

第一，下载 Python 源码，解压。

# 官网下载地址 https://www.python.org/downloadswget https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgzwget https://www.python.org/ftp/python/3.7.3/Python-3.7.3.tgz

# 解压到指定目录 tar zvxf Python-3.7.3.tgz -C /usr/local/src

第二，进入解压的源码路径，编译 python 源码。

export PKG_CONFIG_PATH=/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1/lib/pkgconfig:/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib/pkgconfig:$PKG_CONFIG_PATHexport LD_LIBRARY_PATH=/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1/lib64:/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib:$LD_LIBRARY_PATH

$ ./configure \--enable-optimizations \--prefix=/Bioinfo/Pipeline/SoftWare/Python-3.7.3 \--with-openssl=/Bioinfo/Pipeline/SoftWare/LibDependence/openssl-1.1.1 \CC=/Bioinfo/Pipeline/SoftWare/gcc-4.8.5/bin/gcc \CXX=/Bioinfo/Pipeline/SoftWare/gcc-4.8.5/bin/c++ \LDFLAGS="-L/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1/lib64 -L/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib" \CPPFLAGS="-I/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include" \PKG_CONFIG_PATH="/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1/lib/pkgconfig:/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib/pkgconfig" 

• --enable-optimizations是优化选项（LTO，PGO 等）加上这个 flag 编译后，性能有 10% 左右的优化，但是这会明显的增加编译时间。建议使用这个参数；

• --prefix 声明安装路径；

• 安装多个 python 的版本，如果不开启--enable-shared，指定不同路径即可。当开启--enable-shared时，默认只有一个版本的 python。

• python 3 编译可以使用--with-openssl=DIR指定 OpenSSL 安装路径进行编译的方式解决 OpenSSL 依赖，否则make过程可能出错。

$ make ......The following modules found by detect_modules() in setup.py, have beenbuilt by the Makefile instead, as configured by the Setup files:_abc                  atexit                pwdtime

Failed to build these modules:_ctypes               _hashlib              _ssl

Could not build the ssl module!Python requires an OpenSSL 1.0.2 or 1.1 compatible libssl with X509_VERIFY_PARAM_set1_host().LibreSSL 2.6.4 and earlier do not provide the necessary APIs, https://github.com/libressl-portable/portable/issues/381

......

• make过程如果出现 ModuleNotFoundError: No module named '_ctypes '或者 INFO: Could not locate ffi libs and/or headers 的错误提示，参考下面 的解决方法。

• 如果指定--with-openssl=DIR依然无法解决 ssl 模块的问题，可以参考修改 Modules/Setup.dist 文件(默认这块是注释的，放开注释即可。这块功能是开启 SSL 模块，不然会出现安装完毕后，提示找不到ssl模块的错误)，再执行 configure，修改内容如下：

# Socket module helper for SSL support; you must comment out the other# socket line above, and possibly edit the SSL variable:SSL=/usr/local/ssl_ssl _ssl.c \    -DUSE_SSL -I$(SSL)/include -I$(SSL)/include/openssl \    -L$(SSL)/lib -lssl -lcrypto

第三，Makefile 生后依次在当前路径执行编译和安装命令。

make && make install

第四，安装完成。以上命令执行完毕，且无报错的情况下，我们将默认 python 换将切换至 3.7.3（一般不建议替换，个人建议把自定义安装的 Python bin 路径添加到 PATH 环境变量即可）：

# 替换系统自带的 python（不建议）mv /usr/bin/python /usr/bin/python2ln -s /Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/python3 /usr/bin/python

# 添加新 Python 到 PATH 环境变量（建议）echo "export PATH=/Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin:$PATH" >>~/.bashrcsource ~/.bashrc

运行命令python -V，查看是否出现 3.7.3 的版本，出现即为安装成功。

3. 安装 pip+setuptools

# 下载 setuptools 和 pip 安装程序curl https://bootstrap.pypa.io/get-pip.py -o get-pip.pypython get-pip.py

至此，CentOS Linux release 6.5 下的 python-3.7.3 全部安装完成。如果在安装过程中出现其他的报错，建议把 error 关键信息直接复制到 Google 进行检索，参考其他人的解决方法。

往期精彩：

• Linux 下的动态库、静态库与环境变量

• 手把手教你如何在 Linux 上源码安装最新版本 R

• 非 root 用户手动编译安装 GCC

• 聊一聊 Python 安装中的 --enable-shared

• Python 文件与目录操作方法总结

——The  End——