Difference between revisions of "Installation guide"

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ZENBU is written as a client/server or web2.0 designed system. It is written in c++ and perl for server-side web services and command line tools while the web clients are written in javascript.
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Although the convenience of using the online public zenbu http://fantom.gsc.riken.jp/zenbu has many advantages, we understand that some users will want to install a local copy of ZENBU. This Installation guide is here to help you install a ZENBU server on your machine from source code. This guide will provide you with a working ZENBU server, but will not have a local copy of data. Data will be remotely shared dynamically from the RIKEN ZENBU server.
  
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The ZENBU source code is available for download from our sourceforge page https://sourceforge.net/projects/zenbu
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ZENBU is written as a client/server or web2.0 designed system. It is written in c++ and perl for server-side web services and command line tools while the web clients are written in javascript.
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=== Installing ZENBU version 2.10.0  ===
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In version 2.10 we have simplified the installation process. 
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We introduce a new easy build script to build and install ZENBU on debian/ubuntu linux systems. 
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* phase 1: zenbu_build_debian.sh. The script performs 95% of the necessary operations to get a working zenbu server
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** apt-get operations to install all the dependent libraries and system components
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** builds the zenbu c++ cgi webservices and commandline tools
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** installs the website into /var/www/html
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** installs a basic zenbu.conf file into /etc/zenbu/
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** sets up the mysql zenbu_users database
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* phase 2: you will still need to
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** configure your apache2 server to allow cgi and fcgid exec for zenbu
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** modify the zenbu.conf file for your SMTP email server. Zenbu needs this to send emails to verify user accounts. Without the SMTP, your zenbu will not allow users to make accounts, not allow users to upload data
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** start the zenbu_agent_launcher.sh script in the background as root. This launches the background process for track building and processing uploaded files.
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Please refer to the README_AUTOBUILD file and the build_support directory content for some examples of ways to configure your apache server.
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=== Installing ZENBU version 2.9.x  ===
 
The installation procedure requires several key steps
 
The installation procedure requires several key steps
  
* phase1: get basic server machine setup: apache, fastcgi, mysql server.
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* phase1: [[Installation_guide:_compiling_ZENBU#System_setup | basic server machine setup]]: apache, fastcgi, mysql server.
  
* phase2: compile ZENBU. install all c/c++ and perl libraries
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* phase2: [[Installation_guide:_compiling_ZENBU | compile and install ZENBU]]. including all c/c++ and perl library dependencies
  
* phase3: final tweaking (mysql users, databases, directories, zenbu_config)
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* phase3: [[Installation_guide:_configuration | configuring the server]]
**creating support mysql databases
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** creating support mysql databases
** creating support directory structure
 
** copy ZENBU html/javascript for apache
 
 
** editing the server configuration file
 
** editing the server configuration file
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* phase4: loading data
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** [[Installation_guide:_loading_data#Loading_new_genomes | loading new genomes]]
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** [[Installation_guide:_loading_data#Bulk_command-line_upload_of_datafiles | loading data via the command line]]
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=== upgrading from ZENBU version 2.8.x to 2.9.x ===
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The ZENBU system is designed to use the same databases and directories with different versions of the ZENBU application code. This means that upgrading a ZENBU server to the latest code (with all the new features) is a relatively easy process. 
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Check out the [[Upgrade_guide]] for details on the upgrade procedure.

Latest revision as of 17:08, 20 November 2015

Although the convenience of using the online public zenbu http://fantom.gsc.riken.jp/zenbu has many advantages, we understand that some users will want to install a local copy of ZENBU. This Installation guide is here to help you install a ZENBU server on your machine from source code. This guide will provide you with a working ZENBU server, but will not have a local copy of data. Data will be remotely shared dynamically from the RIKEN ZENBU server.

The ZENBU source code is available for download from our sourceforge page https://sourceforge.net/projects/zenbu ZENBU is written as a client/server or web2.0 designed system. It is written in c++ and perl for server-side web services and command line tools while the web clients are written in javascript.

Installing ZENBU version 2.10.0

In version 2.10 we have simplified the installation process. We introduce a new easy build script to build and install ZENBU on debian/ubuntu linux systems.

  • phase 1: zenbu_build_debian.sh. The script performs 95% of the necessary operations to get a working zenbu server
    • apt-get operations to install all the dependent libraries and system components
    • builds the zenbu c++ cgi webservices and commandline tools
    • installs the website into /var/www/html
    • installs a basic zenbu.conf file into /etc/zenbu/
    • sets up the mysql zenbu_users database
  • phase 2: you will still need to
    • configure your apache2 server to allow cgi and fcgid exec for zenbu
    • modify the zenbu.conf file for your SMTP email server. Zenbu needs this to send emails to verify user accounts. Without the SMTP, your zenbu will not allow users to make accounts, not allow users to upload data
    • start the zenbu_agent_launcher.sh script in the background as root. This launches the background process for track building and processing uploaded files.

Please refer to the README_AUTOBUILD file and the build_support directory content for some examples of ways to configure your apache server.


Installing ZENBU version 2.9.x

The installation procedure requires several key steps

upgrading from ZENBU version 2.8.x to 2.9.x

The ZENBU system is designed to use the same databases and directories with different versions of the ZENBU application code. This means that upgrading a ZENBU server to the latest code (with all the new features) is a relatively easy process.

Check out the Upgrade_guide for details on the upgrade procedure.