Appion

h1. Install the Web Interface

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

h2. 1. Install pyami

TODO: put the prereqs for this in Web Preq page rather than linking to the processing page.

If you have not yet installed Leginon/Appion python packages on this server, the web interface will at least need the myami/pyami package to do MRC to JPEG conversion.  First [[Install supporting packages|install the supporting packages]].  Then install myami/pyami as follows:

<pre>

cd myami/pyami

sudo python setup.py install

</pre>

This will install the script "mrc2any" into /usr/bin/mrc2any (for typical linux system).  You can customize the location with options to the setup.py command.

To be sure where it was installed, run:

<pre>

which mrc2any

</pre>

You will need to know that location when configuring below.

h2. 2. Copy the myami/myamiweb directory to your Apache web directory

Example:

<pre>

cd myami

#CentOS example

sudo cp -vr myamiweb /var/www/html/ 

#this is temporary for setup, revert to 755 when finished with this page

sudo chmod 777 /var/www/html/myamiweb  

#if you have SELinux enabled this command will help

sudo chcon -R --type=httpd_sys_content_t /var/www/html

</pre>

h2. 3. 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

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

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

 

*Tips:*

# You can ignore any warnings about a missing 'ssh2' module at this time. This module is needed for Appion installations, however installation instructions are available later in the installation process under [[appion:Setup Remote Processing]].

# You need to know your database setup before you start.  If you have been using the parameters in this instruction, here is a [[Explanation of Sample Names|summary]].

# To discover what the Apache user is:<pre> egrep -iw --color=auto 'user|group' /etc/httpd/conf/httpd.conf</pre>

# You also need to decide whether you would like to enable the [[appion:What does User Authentication do to myamiweb|user management system]].

h3. Manual configuration instructions (Advanced User)

Go to [[Install the Web Interface Advanced]] for the advanced configuration.

h2. 4. Revert permissions

<pre>

sudo chmod 755 /var/www/html/myamiweb

</pre>

h2. 5. Test the installation

Visit http://yourhost/myamiweb  or http://localhost/myamiweb to confirm functionality.

You may also browse to the automatic web server troubleshooter at: http://localhost/myamiweb/test/checkwebserver.php

h2. 6. Turn off error checking in php.ini

Edit the following items in php.ini (found as /etc/php.ini on CentOS and /etc/php5/apache2/php.ini on SuSE) so that they look like the following:

bq. display_errors = Off

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[[Install the MRC PHP Extension|< Install the MRC PHP Extension]] | [[Install phpMyAdmin|Install phpMyAdmin >]]

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