Appion

h1. Install the Web Interface

Install Leginon and Appion web tools for viewing images and performing image processing through the web server.

If you are installing your web server on a different machine than your processing server, 

you need to download the myami code.

*TODO:* add a link to the myami code 

h2. 1. Move the myami/myamiweb directory to your Apache web directory

Example:

<pre>

> cd [webdirectory]   // /var/www/html in this example

> cp [path_to_myami_download_location]/myami/myamiweb .

</pre>

h2. 2. Configure your installation 

There is a setup wizard available to help you set the configuration parameters for your installation. If you prefer not to use the wizard, there are instructions for manually editing the configuration file. If this is your first time creating the web tool configuration file, we recommend using the setup wizard.

h3. Configuration using the setup wizard

Run the online setup wizard by visiting http://yourhost/myamiweb/setup to create the myami website’s config file. 

The setup wizard will also check your database connection, create required database tables, and perform default data initialization.

h3. Manual configuration instructions (Advanced User)

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.

* 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");

<pre>

define('BASE_PATH',"myamiweb"); 

</pre>

* myamiweb login system

<pre>

// Browse to the administration tools in myamiweb prior to 

// changing this to true to populate DB tables correctly.

define('ENABLE_LOGIN', false);	

</pre>

* Administrator email title and email address

<pre>

define('EMAIL_TITLE', 'The name of your institute');

define('ADMIN_EMAIL', "example@institute.edu");

</pre>

* SMTP Server setup (not required but recommended):

<pre>

define('ENABLE_SMTP', false);

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

</pre>

* When SMTP server requires authentication

<pre>

// --- 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', "");

</pre>

* Setup your MySQL database server parameters:

<pre>

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

</pre>

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

<pre>

addplugin("processing");

</pre>

* Add processing host information

<pre>

// --- 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' => );

</pre>

* Microscope spherical aberration constant

<pre>

$DEFAULTCS = "2.0";

</pre>

* IMAGIC and Other features:

<pre>

// 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);

</pre>

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

h2. 3. Test the set-up by visiting http://yourhost/myamiweb

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[[Install the MRC PHP Extension|< Install the MRC PHP Extension]] | [[Potential Problems|Potential Problems >]]

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