Appion

h1. Start with existing CentOS 5.3 64-bit installation

{{>toc}}

h2. 3 Download additional software 

[[Download additional Software]]

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h2. 4 MRC PHP Extension Installation and Testing

[[MRC PHP Extension Installation and Testing]]

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h2. 5 Setup MySQL (appiondata) databases 

[[Setup MySQL database]]

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h2. 6 Compile and setup Appion python programs 

[[Setup Appion programs]]

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h2. 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.

h3. Install MRC Tools 

h4. Compile MRC tools 

* Go to your php devel directory and untar the archive

* If unsure where it is, use info.php to find it under *extension_dir*

<pre>

$ cd /usr/include/php/ext/

$ sudo mkdir mrc

$ sudo chmod 777 mrc

$ sudo chown $USER mrc

</pre>

* Unpackage MRC Tools from http://emg.nysbc.org/software/mrctools/

<pre>

$ tar zxvf ~/php_mrc.tgz

$ cd mrc/

</pre>

* Compile and install the MRC module

<pre>

$ phpize

$ ./configure 

$ make

$ sudo make install

</pre>

h4. Configure PHP for MRC Tools 

* Confirm the location of "additional .ini files parsed" from info.php web page (/etc/php.d in this example)

* Create a file called  "mrc.ini" in this directory.

<pre>

$ sudo nano /etc/php.d/mrc.ini

</pre>

* Add these lines in the file "mrc.ini" to make mrc.so an extension

<pre>

; Enable mrc extension module

extension=mrc.so

</pre>

* To test MRC tools, go to this website:

http://emg.nysbc.org/software/mrctools/mrc_so.php

h3. Configure PHP 

* increase the memory limit, EM images are big 64MB:

<pre>

memory_limit = 256M; Maximum amount of memory

</pre>

* Turn error display on:

<pre>

display_errors = On

</pre>

<pre>

error_reporting = E_ALL & ~E_NOTICE & ~E_WARNING

</pre>

* restart the webserver

<pre>

$ sudo /sbin/service httpd restart

</pre>

h3. Install DBEM and project php source 

Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]]

h3. Configuration 

h4. configure apache 

* allow REMOTE_HOST lookups in apache

<pre>

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

</pre>

* turn _HostnameLookups_ to On

<pre>

HostnameLookups On

</pre>

* restart the webserver

<pre>

$ sudo /sbin/service httpd restart

</pre>

h4. configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing 

Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]]

h3. Initialize database tables from the web tools 

Please consult [[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Create a test project and processing database]]

h3. Potential problems 

h4. Firewall settings 

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

<pre>

$ system-config-securitylevel

</pre>

h4. Security-enhanced linux 

"Security-enhanced linux (SELinux)":http://en.wikipedia.org/wiki/Security-Enhanced_Linux  may be preventing your files from loading. To fix this run the following command:

<pre>

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

</pre>

see "this website":http://docs.fedoraproject.org/selinux-apache-fc3/sn-simple-setup.html  for more details on SELinux

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h2. 8 Install external packages 

*Please follow individual package installation instruction provided with them*

h3. Compile Xmipp for OpenMPI 

[[Install Xmipp]]

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h2. 9 Install a PBS job submission system

[[Install PBS]]

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h2. 10 Do testing (Start at 4 of any flavor)

[[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Get started with a project]]

This has some repeated information.

Basically need to do the following:

# Add a group

# Add a user

# Add instruments

# Create a project

# Create the project database

# Upload images to a new session

# View the images

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