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 对 Python 的源码编译安装进行了一下简单的总结,记录如下


1. 安装 Python-3.7.3


1.1 安装环境


os : CentOS Linux release 6.5 (x86_64) 
gcc: 4.8.5 20150623



1.2 安装步骤


如果您拥有 root 权限,请执以下依赖安装:

yum install zlib
yum install zlib-devel
yum install openssl
yum install openssl-devel
yum install libffi
yum install libffi-devel
yum install readline readline-devel sqlite sqlite-devel tk-devel 


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


1.2.1 ssl 依赖


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。



1.2.2 ctypes 依赖


在 CentOS 6.x 安装 libffi-devel 的时候出现以下问题:


$ yum install -y libffi-devel
Loaded plugins: product-id, refresh-packagekit, search-disabled-repos, security, subscription-manager
This system is not registered to Red Hat Subscription Management. You can use subscription-manager to register.
Setting up Install Process
cdrom                                                                                                                                         | 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.rpm
Retrieving http://mirror.centos.org/centos/6/os/x86_64/Packages/libffi-devel-3.0.5-3.2.el6.x86_64.rpm
warning: /var/tmp/rpm-tmp.V9ihbu: Header V3 RSA/SHA256 Signature, key ID c105b9de: NOKEY
Preparing...                ########################################### [100%]
   1:libffi-devel           ########################################### [100%]
[root@log01 ~]# rpm -qa|grep libffi
libffi-3.0.5-3.2.el6.x86_64
libffi-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 



1.2.3 pygraphviz 依赖


$ /Bioinfo/Pipeline/SoftWare/Python-3.7.3/bin/pip3 install pygraphviz
Collecting pygraphviz
  Using cached https://files.pythonhosted.org/packages/7e/b1/d6d849ddaf6f11036f9980d433f383d4c13d1ebcfc3cd09bc845bda7e433/pygraphviz-1.5.zip
Installing 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:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include:$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH=/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/include:$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.zip
Installing collected packages: pygraphviz
  Running setup.py install for pygraphviz ... done
Successfully installed pygraphviz-1.5



1.3 编译安装 Python-3.7.3


第一,下载 Python 源码,解压。

# 官网下载地址 https://www.python.org/downloads
wget https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgz
wget 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:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=/Bioinfo/Pipeline/SoftWare/LibDependence/libffi-3.2.1/lib64:/Bioinfo/Pipeline/SoftWare/graphviz-2.40.1/lib:$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" 



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


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

......


image.png


# 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/python2
ln -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" >>~/.bashrc
source ~/.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。



1.4. 安装 pip+setuptools


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




2. 安装 Python-3.6.9


2.1 安装环境



2.2 No module named '_bz2'


在 CentOS 7 中安装 Python-3.6.9 中发现 make 过程中一直提示:“ModuleNotFoundError: No module named '_bz2'”,尽管 sudo yum install bzip2 bzip2-devel 已经安装了 bzip2 的依赖,问题还是不得其解。最后参考 stackoverflow 上的《Correctly building local python3, with bz2 support》,终于解决问题,下面记录一下。


2.3 手动安装 bzip2

wget https://nchc.dl.sourceforge.net/project/bzip2/bzip2-1.0.6.tar.gz
tar zvxf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6
make -f Makefile_libbz2_so  # 这一步是生成 libbz2.so.1.0.6 的动态库文件
make 
make install PREFIX=/usr/local/software/bzip2-1.0.6
cp libbz2.so.1.0.6 /usr/local/software/bzip2-1.0.6/lib/

几点说明:


2.4 编译安装 Python-3.6.9


$ wget https://www.python.org/ftp/python/3.6.9/Python-3.6.9.tgz
$ tar zvxf Python-3.6.9.tgz
$ cd Python-3.6.9
$ ./configure --enable-optimizations --prefix=/usr/local/software/python-3.6 CFLAGS="-I/usr/local/software/bzip2-1.0.6/include" LDFLAGS="-L/usr/local/software/bzip2-1.0.6/lib"
$ make
$ make install



F. 参考资料


  1. 行者无疆-ITer,python2.7 源码编译安装》, 博客园
  2. Scott Frazer,《How do I compile Python 3.4 with custom OpenSSL?》, Stack Overflow