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');
   

   
    
7. Add Redux Image server parameters
   

   define('SERVER_HOST',"localhost")
   define('SERVER_PORT',"55123");
   

   
   The server port chosen should match the value found in redux.log when the redux server is started.

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
   processing host is the computer with pbs server running (i.e. the head node of a computer cluster if applicable)
    
   Appion version 2.2 and later:
   The following code should be added and modified for each processing host available.
   

   $PROCESSING_HOSTS[] = array(
   'host' => 'LOCAL_CLUSTER_HEADNODE.INSTITUTE.EDU', // for a single computer installation, this can be 'localhost'    
   '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' => 'USERPASSWORD', // Appion currently supports 'USERPASSWORD'.  'SHAREKEY' is possible, but not preferable. 
   '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' (not supported 
   '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";
   

   
    
5. Redux server information
    
   This is a very new feature, post Appion 2.2, so you only need this if you are running the trunk or 2.2-redux.
   The Redux server replaces the old mrc_php module and will be released in Appion version 3.0.
   Information on redux parameters to add to the config.php

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

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