腾飞基因项目 安装配置文档-Ubuntu版
腾飞基因项目 安装配置文档-Ubuntu版
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腾飞基因项目 安装配置文档-Ubuntu版
腾飞基因项目 安装配置文档-Ubuntu版
一、buildout Plone 生产环境
1、创建用户组，用户,并为该用户账号授权sudo
以root身份登陆系统
root@ubuntu1804:~# adduser --home /home/plone plone plone
添加用户demo到sudo组
root@ubuntu1804:~# usermod –aG sudo plone
2、用plone用户登陆系统，安装Plone依存的系统库
plone@ubuntu1804:~$ sudo apt-get update
plone@ubuntu1804:~$ sudo apt-get install python-setuptools python-dev build-essential libssl-dev libxml2-dev libxslt1-dev libbz2-dev libjpeg62-dev zlib1g-dev libreadline-dev wv poppler-utils libssl-dev libffi-dev python-matplotlib python-gtk2 fonts-wqy-microhei fonts-wqy-zenhei libreoffice apache2 varnish p7zip python-docutils libncurses5-dev libncursesw5-dev
plone@ubuntu1804:~$ sudo apt-get install libreoffice-help-common
varnish 我们采用自编译版本，禁止掉系统 varnish:
plone@ubuntu1804:~$ sudo systemctl stop varnish
plone@ubuntu1804:~$ sudo systemctl disable varnish
3、在用户主目录下，创建目录workspace，下载并编译安装python2.7.x最新版，本文是python 2.7.15
plone@ubuntu1804:~$ mkdir ~/workspace
plone@ubuntu1804:~$ mkdir workspace/downloads plone@ubuntu1804:~$ cd workspace/downloads
去到python.org官方网站下载：
plone@ubuntu1804:~/workspace/downloads$ wget https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgz
解压缩，编译安装python2.7.15
plone@ubuntu1804:~/workspace/downloads$ tar -zxvf Python-2.7.15.tgz
plone@ubuntu1804:~/workspace/downloads$ cd Python-2.7.15 plone@ubuntu1804:~/workspace/downloads/Python-2.7.15$ ./configure --prefix=/home/plone/workspace/python2715 --enable-unicode=ucs4 --enable-optimizations plone@ubuntu1804:~/workspace/downloads/Python-2.7.15$ make plone@ubuntu1804:~/workspace/downloads/Python-2.7.15$ make install
4、下载get-pip.py，用python2.7.15 安装pip
plone@ubuntu1804:~/workspace/downloads$ curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
plone@ubuntu1804:~/workspace/downloads$ cd ~/workspace/python2715/
给python2715安装pip
plone@ubuntu1804:~/workspace/python2715$ bin/python2 ~/downloads/get-pip.py
5、克隆gene.buildout生产站点配置项目到用户主目录workspace
plone@ubuntu1804:~/workspace/python2715$ cd ~/workspace
plone@ubuntu1804:~/workspace$ git clone -b master --single-branch https://github.com/Ascendasgenomics/gene.buildout.git gene
6、用pip2 安装virtualenv，并创建python虚拟环境
plone@ubuntu1804:~/workspace$ cd ~/workspace/python2715/
plone@ubuntu1804:~/workspace/python2715$ bin/pip2 install virtualenv
plone@ubuntu1804:~/workspace/python2715$ bin/virtualenv /home/plone/workspace/gene
7、激活虚拟环境
plone@ubuntu1804:~/workspace/python2715$ cd ~/workspace/gene
plone@ubuntu1804:~/workspace/gene$ source bin/activate
8、编译安装部分三方模块到虚拟环境python路径，包括但不限于zc.buildout、setuptools等
(gene) plone@ubuntu1804:~/workspace/gene$
(gene) plone@ubuntu1804:~/workspace/gene$ pip2 install --trusted-host mirrors.aliyun.com -i http://mirrors.aliyun.com/pypi/simple -r requirements-5-1.txt
9、建立buildou缓存目录，运行buildout配置命令：
(gene) plone@ubuntu1804:~/workspace/gene$ cd ..
(gene) plone@ubuntu1804:~/workspace$ tar -zxvf downloads/build_eggs.tar.gz
注意：解压缩后会生成一个名为.buildout的目录，默认是隐藏的。
10、释放开发包到 /home/plone/workspace/gene目录
(gene) plone@ubuntu1804:~/workspace$ cd gene
(gene) plone@ubuntu1804:~/workspace/gene$ tar -zxvf ../downloads/src.tar.gz
运行buildout
(gene) plone@ubuntu1804:~/workspace/gene$ bin/buildout -Nvvv -c deploy_haproxy.cfg
10、通过supervisor启动各服务进程
(gene) plone@ubuntu1804:~/workspace/gene$ sudo bin/supervisord
检测各服务进程
(gene) plone@ubuntu1804:~/workspace/gene$ bin/supervisorctl status
二、配置apache2
启用某些模块
(gene) plone@ubuntu1804:~$ sudo a2enmod rewrite
(gene) plone@ubuntu1804:~$ sudo a2enmod proxy
(gene) plone@ubuntu1804:~$ sudo a2enmod expires
(gene) plone@ubuntu1804:~$ sudo a2enmod deflate
在 /etc/apache2/site-available下增加文件demo.gene.org.conf，这个用于主站日常访问
(gene) plone@ubuntu1804:~$ cd /etc/apache2/site-available/
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo touch demo.gene.org.conf
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo vi demo.gene.org.conf
输入如下内容：
<VirtualHost *:80>
<Proxy *>
Allow from www.gene.org
</Proxy>
ServerName www.gene.org
ServerAlias gene.org
RewriteEngine on
RewriteRule ^(.*)$ http://localhost:8581/VirtualHostBase/http/192.168.0.185:80/Plone/VirtualHostRoot/$1 [L,P]
ExpiresActive On
ExpiresByType image/gif A3600
ExpiresByType image/png A3600
ExpiresByType image/image/vnd.microsoft.icon A3600
ExpiresByType image/jpeg A3600
ExpiresByType text/css A3600
ExpiresByType text/javascript A3600
ExpiresByType application/x-javascript A3600
<IfModule mod_deflate.c>
SetOutputFilter DEFLATE
</IfModule>
</virtualHost>
在 /etc/apache2/site-available下增加文件zmi.gene.org.conf，这个用于ZMI管理，如添加站点等
(gene) plone@ubuntu1804:~$ cd /etc/apache2/site-available/
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo touch zmi.gene.org.conf
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo vi zmi.gene.org.conf
输入如下内容：
<VirtualHost *:80>
<Proxy *>
Allow from zmi.gene.org
</Proxy>
ServerName zmi.gene.org
ProxyPass / http://localhost:8883/
ProxyPassReverse / http://localhost:8883/
ProxyPreserveHost On
</VirtualHost>
在 /etc/apache2/site-enable下增加 符号连接：zmi.gene.org.conf
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo ln -s /etc/apache2/site-available/zmi.gene.org.conf /etc/apache2/site-enable/zmi.gene.org.conf
编辑apache配置文件：
sudo vi /etc/apache2/apache2.conf
调整Timeout参数：
#
PidFile ${APACHE_PID_FILE}
#
# Timeout: The number of seconds before receives and sends time out.
#
Timeout 600
#
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to "Off" to deactivate.
#
KeepAlive On
#
# MaxKeepAliveRequests: The maximum number of requests to allow
# during a persistent connection. Set to 0 to allow an unlimited amount.
# We recommend you leave this number high, for maximum performance.
#
MaxKeepAliveRequests 100
-- INSERT --
重启apache:
(gene) plone@ubuntu1804:/etc/apache2/site-available$ sudo systemctl restart apache2.service
三、创建report目录并安装字体
创建report默认保存目录，并设置权限：
(gene) plone@ubuntu1804:/etc/apache2/site-available$ cd
(gene) plone@ubuntu1804:~$ sudo mkdir -p /srv/report_files
(gene) plone@ubuntu1804:~$ sudo chown -R plone:plone /srv/report_files
安装字体：
(gene) plone@ubuntu1804:~$ cd workspace/downloads
(gene) plone@ubuntu1804:~/workspace/downloads$ unzip fonts.zip
(gene) plone@ubuntu1804:~/workspace/downloads$ sudo mv fonts/truetype /usr/share/fonts/
(gene) plone@ubuntu1804:~/workspace/downloads$ sudo mv fonts/opentype /usr/share/fonts/
四、检查libreoffice 安装是否成功
运行python3
(gene) plone@ubuntu1804:~$ cd workspace/gene
(gene) plone@ubuntu1804:~/workspace/gene$ deactive
plone@ubuntu1804:~/workspace/gene$ /usr/bin/python3
尝试导入uno 和 unohelper,应不报错，如下：
Python 3.6.8 (default, Apr 2 2020, 13:34:55)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import uno
>>> import unohelper
>>>
五、添加并配置Plone站点，完成gene项目初始化
- 添加站点：打开浏览器，访问http://zmi.gene.org/，输入管理员账户admin及密码，按照提示添加站点，站点id默认为Plone。
- 安装策略包，完成gene项目初始化
打开浏览器访问http://demo.gene.org/输入管理员账户admin及密码,登录后，点击左下角菜单中的“网站设置”。
在 “常规”组里面点击“附加组件”，在“可启用附加组件”中寻找gene.policy，找到后，点击其后的 “安装”按钮即可。
六、设置相关服务自启动
添加systemd管理的自启动服务
1、自启动supervisord
sudo touch /etc/systemd/system/supervisord.service
sudo vi /etc/systemd/system/supervisord.service
填充如下内容：
[Unit]
Description=Supervisor Monitor
After=network.target
After=syslog.target
[Install]
WantedBy=multi-user.target
[Service]
User=root
Group=root
PIDFile=/home/plone/workspace/gene/var/supervisord.pid
# Disable service start and stop timeout logic of systemd for supervisor service.
TimeoutSec=0
Type=forking
# Start main service
ExecStart=/home/plone/workspace/gene/bin/supervisord
ExecStop=/home/plone/workspace/gene/bin/supervisorctl shutdown
StartLimitBurst=2
StartLimitInterval=30
允许supervisord 作为deamon自动启动：
sudo systemctl enable supervisord.service2、自启动libreoffice
sudo touch /etc/systemd/system/libreoffice.service
sudo vi /etc/systemd/system/libreoffice.service
填充如下内容：
[Unit]
Description=Control headless soffice instance
After=network.target
[Service]
Type=simple
ExecStart=/usr/bin/soffice --invisible --headless \
'--accept=socket,host=127.0.0.1,port=2002;urp; '
--pidfile=/var/run/soffice.pid
RestartSec=5
PIDFile=/var/run/soffice.pid
[Install]
WantedBy=multi-user.target
允许libreoffice 作为deamon自动启动：
sudo systemctl enable libreoffice.service补充：，需要注意的是，Python 2已于2020年1月1日停止维护，因此Ubuntu 20.04默认情况下可能不再提供Python 2的开发包。如果你确实需要Python 2的开发环境，可以考虑以下步骤：
-
添加旧版本的PPA（个人包档案）： 你可以添加一个包含Python 2的PPA，例如deadsnakes PPA：
sudo add-apt-repository ppa:deadsnakes/ppa sudo apt update