Start with existing CentOS 5.3 64-bit installation¶

• Table of contents
• Start with existing CentOS 5.3 64-bit installation
  • 3 Download additional software
  • 4 MRC PHP Extension Installation and Testing
  • 5 Setup MySQL (appiondata) databases
  • 6 Compile and setup Appion python programs
  • 7 Install webpages (myamiweb)
    • Install DBEM and project php source
    • Configuration
      • configure apache
      • configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing
    • Initialize database tables from the web tools
    • Potential problems
      • Firewall settings
      • Security-enhanced linux
  • 8 Install external packages
    • Compile Xmipp for OpenMPI
  • 9 Install a PBS job submission system
  • 10 Do testing (Start at 4 of any flavor)

3 Download additional software¶

Download additional Software

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4 MRC PHP Extension Installation and Testing¶

MRC PHP Extension Installation and Testing

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5 Setup MySQL (appiondata) databases¶

Setup MySQL database

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6 Compile and setup Appion python programs¶

Setup Appion programs

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7 Install webpages (myamiweb)¶

Refer to Web Server Installation

TODO: The next steps have already been completed, grab any extra info from here and move to other location.

Install DBEM and project php source¶

Please consult the other Install guide

Configuration¶

configure apache¶

• allow REMOTE_HOST lookups in apache

$ sudo nano /etc/httpd/conf/httpd.conf

• turn HostnameLookups to On

HostnameLookups On

• restart the webserver

$ sudo /sbin/service httpd restart

configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing¶

Please consult the other Install guide

Initialize database tables from the web tools¶

Please consult Create a test project and processing database

Potential problems¶

Firewall settings¶

You may need to configure your firewall to allow incoming HTTP (port 80) and MySQL (port 3306) traffic:

$ system-config-securitylevel

Security-enhanced linux¶

Security-enhanced linux may be preventing your files from loading. To fix this run the following command:

$ sudo /usr/bin/chcon -R -t httpd_sys_content_t /var/www/html/

see this website for more details on SELinux

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8 Install external packages¶

Please follow individual package installation instruction provided with them

Compile Xmipp for OpenMPI¶

Install Xmipp

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9 Install a PBS job submission system¶

Install PBS

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10 Do testing (Start at 4 of any flavor)¶

Get started with a project
This has some repeated information.
Basically need to do the following:

1. Add a group
2. Add a user
3. Add instruments
4. Create a project
5. Create the project database
6. Upload images to a new session
7. View the images
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