Install the Web Interface Advanced¶

Manual configuration instructions (Advanced User)¶

Note: You may skip this section if you configured your installation with the setup wizard at http://localhost/myamiweb/setup.

Copy config.php.template to config.php and edit the latter by adding these parameters:
"config.php" should be located in /var/www/html/myamiweb/ on CentOS and /srv/www/htdocs/myamiweb/ on SuSE.

1. define site base path
   This should be changed if the myamiweb directory is located
   in a sub-directory of the Apache web directory.
   ex. myamiweb is in /var/www/html/applications/myamiweb/ then
   change to define('BASE_PATH',"applications/myamiweb");
    
   

   define('BASE_PATH',"myamiweb"); 
   

   
    
2. myamiweb login system
   

   // Browse to the administration tools in myamiweb prior to 
   // changing this to true to populate DB tables correctly.
   define('ENABLE_LOGIN', false);    
   

   
    
3. Administrator email title and email address
   

   define('EMAIL_TITLE', 'The name of your institute');
   define('ADMIN_EMAIL', "example@institute.edu");
   

   
    
4. SMTP Server setup (not required but recommended):
   

   define('ENABLE_SMTP', false);
   define('SMTP_HOST', 'mail.institute.edu');    //your smtp host
   

   
    
   1. When SMTP server requires authentication
      

      // --- Check this with your email administrator -- //
      // --- Set it to true if your SMTP server requires authentication -- //
      define('SMTP_AUTH', false);
      
      // --- If SMTP_AUTH is not required(SMTP_AUTH set to false, -- //
      // --- no need to fill in 'SMTP_USERNAME' & SMTP_PASSWORD -- //
      define('SMTP_USERNAME', "");
      define('SMTP_PASSWORD', "");
      

      
       
5. Setup your MySQL database server parameters:
   

   define('DB_HOST', "");        // DB Host name
   define('DB_USER', "");        // DB User name
   define('DB_PASS', "");        // DB Password
   define('DB_LEGINON', "");    // Leginon database name
   define('DB_PROJECT', "");    // Project database name
   

   
    
6. Enable Image Cache
   If you want to use caching function for faster image loading time in image viewer, change 'ENABLE_CACHE' to true.
   You can change the 'CACHE_PATH' to other location, but make sure the apache user has write access to this folder.
   

   // --- Enable Image Cache --- //
   define('ENABLE_CACHE', true);
   // --- caching location --- //
   // --- please make sure the apache user has write access to this folder --- //
   define('CACHE_PATH', '/srv/www/cache/');
   define('CACHE_SCRIPT', WEB_ROOT.'/makejpg.php');
   

Additional parameters needed for Appion Installations only:¶

1. Enable the processing plug-in by uncommenting out the following line in the file`myamiweb/config.php`
   

   addplugin("processing");
   

   
    
2. IMAGIC and Other features:
   

   // Check if IMAGIC is installed and running, otherwise hide all functions
   define('HIDE_IMAGIC', false);
   
   // hide processing tools still under development.
   define('HIDE_FEATURE', true);
   

   
    
3. Add processing host information
    
   Appion version 2.2 and later:
   The following code should be added and modified for each processing host available.
   

   $PROCESSING_HOSTS[] = array(
   'host' => 'myhost.inst.edu',    
   'nproc' => 32,  // number of processors available on the host, not used
   'nodesdef' => '4', // default number of nodes used by a refinement job
   'nodesmax' => '280', // maximum number of nodes a user may request for a refinement job
   'ppndef' => '32', // default number of processors per node used for a refinement job
   'ppnmax' => '32', // maximum number of processors per node a user may request for a refinement job
   'reconpn' => '16', // recons per node, not used 
   'walltimedef' => '48', // default wall time in hours that a job is allowed to run
   'walltimemax' => '240', // maximum hours in wall time a user may request for a job
   'cputimedef' => '1536', // default cpu time in hours a job is allowed to run (wall time x number of cpu's) 
   'cputimemax' => '10000', // maximum cpu time in hours a user may request for a job
   'memorymax' => '', // the maximum memory a job may use
   'appionbin' => 'bin/', // the path to the myami/appion/bin directory on this host
   'appionlibdir' => 'appion/', // the path to the myami/appion/appionlib directory on this host
   'baseoutdir' => 'appion', // the directory that processing output should be stored in
   'localhelperhost' => '', // a machine that has access to both the web server and the processing host file systems to copy data between the systems
   'dirsep' => '/', // the directory separator used by this host
   'wrapperpath' => '', // advanced option that enables more than one Appion installation on a single machine, contact us for info 
   'loginmethod' => 'SHAREDKEY', // Appion currently supports 'SHAREDKEY' or 'USERPASSWORD' 
   'loginusername' => '', // if this is not set, Appion uses the username provided by the user in the Appion Processing GUI
   'passphrase' => '', // if this is not set, Appion uses the password provided by the user in the Appion Processing GUI
   'publickey' => 'rsa.pub', // set this if using 'SHAREDKEY'
   'privatekey' => 'rsa'      // set this if using 'SHAREDKEY'
   );
   

   
    
   Appion version 2.1 and prior:
   

   // --- Please enter your processing host information associate with -- //
   // --- Maximum number of the processing nodes                                    -- //
   // --- $PROCESSING_HOSTS[] = array('host' => 'host1.school.edu', 'nproc' => 4); -- //
   // --- $PROCESSING_HOSTS[] = array('host' => 'host2.school.edu', 'nproc' => 8); -- //
   
   // $PROCESSING_HOSTS[] = array('host' => '', 'nproc' => );
   

   
    
4. Microscope spherical aberration constant
    
   Not needed for Appion version 2.2 and later. Version 2.1 and earlier only:
   

   $DEFAULTCS = "2.0";
   

We will not include the cluster registration now. It is covered in the last part of this document.

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