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Start with existing CentOS installation » History » Version 66

Amber Herold, 04/06/2010 12:43 PM

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h1. Start with existing CentOS 5.3 64-bit installation
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{{>toc}}





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h2. 3 Download additional software 





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[[Download additional Software]]





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h2. 4 MRC PHP Extension Installation and Testing





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[[MRC PHP Extension Installation and Testing]]





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h2. 5 Setup MySQL (appiondata) databases 





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[[Setup MySQL database]]





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h2. 6 Compile and setup Appion python programs 





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[[Setup Appion programs]]





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h2. 7 Install webpages (myamiweb)





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Refer to [[Web Server Installation]]





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*TODO:* The next steps have already been completed, grab any extra info from here and move to other location.





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* To test MRC tools, go to this website:





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





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h3. Install DBEM and project php source 





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





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h3. Configuration 





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h4. configure apache 





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* allow REMOTE_HOST lookups in apache





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<pre>





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





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</pre>





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* turn _HostnameLookups_ to On





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<pre>





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HostnameLookups On





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</pre>





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* restart the webserver





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<pre>





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$ sudo /sbin/service httpd restart





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</pre>





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h4. configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing 





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





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h3. Initialize database tables from the web tools 





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





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h3. Potential problems 





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h4. Firewall settings 





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





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<pre>





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$ system-config-securitylevel





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h4. Security-enhanced linux 





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"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:





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<pre>





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





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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 





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*Please follow individual package installation instruction provided with them*





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h3. Compile Xmipp for OpenMPI 





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[[Install Xmipp]]





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h2. 9 Install a PBS job submission system





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[[Install PBS]]





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





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





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This has some repeated information.





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Basically need to do the following:





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# Add a group





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# Add a user





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# Add instruments





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# Create a project





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# Create the project database





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# Upload images to a new session





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# View the images





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