• MySQL
  
  
  • MySQL-server
  • MySQL-client
  • MySQL-shared
  • MySQL-devel
  
  But be sure to read and understand the upgrade process. More here
  
  
• PHP
  
  Centos 4.2 comes with PHP 4.3.9, but if you want to check you version type:
  
  
  • php --version
    
  • If your version is lower than PHP 4 then install this two rpms:
    Make sure that MySQL and GD clients are compiled in this version. The version origally shipped with Centos4.2 is fine
    • PHP-4.3.11-2.8
    • PHP-MySQL-client-4.3.11-2.8
  
  
  
• Apache
  
  
  • Finally you will have to check if this line is present AND uncommented either in the apache config (httpd.conf) LoadModule section or
  • Check in the /etc/httpd/conf.d/php.conf file that these lines are uncommented and
    
    
    • LoadModule php4_module modules/libphp4.so
      
      
    • AddType application/x-httpd-php-source .php
      
      
    • DirectoryIndex index.php

Step 2:

Modification of MySQL, PHP and Apache:

• MySQL should work without problems. You can edit the my.cnf file located here, /etc/my.cnf accordingly to MySQL ducomentation there
  
  
• PHP
  
  In the file php.ini everything after a semi-colon " ; " will NOT be read by PHP.
  
  
  • Change the line: allow_call_time_pass_reference = Off to
    allow_call_time_pass_reference = On
    
    
  • Then you will have to decide:
    
    1. How long you will let PHP run to execute a script. To do so change the number of second at this line
       max_execution_time = 30
       to something bigger like 300 or even 3600
    2. How much memory a script can consume at:
       memory_limit = 64
       Change 64M to something more close to 512M (depending of your machine's RAM)
       
       
  • In order to debug problems, it is wise to change these lines:
    
    1. error_reporting = E_ALL to error_reporting = E_ALL & ~E_NOTICE
    2. display_errors = Off to display_errors = On
    3. ; error_log = filename could be something like that
       error_log = /var/log/php_errors. The name "php_errors" could be replaced by something of your choice.
       
       
  • If you plan to upload big file you should change these line
    1. post_max_size = 8M to post_max_size = 80M
    2. upload_max_filesize = 2M to upload_max_filesize = 80M
       
       
  • For security reason you should turn this feature on:
    magic_quotes_gpc = Off to magic_quotes_gpc = On
    
    
  • Change this line:
    dbx.colnames_case = "lowercase" to dbx.colnames_case = "unchanged"
    
    
  • Allow the garbage collection to happen more often by reducing the divisor here
    session.gc_dvisor = 1000 to session.gc_divisor = 100
    
    
  • And finally Allow bug_compat to happen:
    session.bug_compat_42 = 0 session.bug_compat_42 = 1
  
  
• Apache Having SELinux activated per default, the apache server will NOT serve any file outside /var/www/html
  The easiest solution is to switch off SELinux by changing the configuration file /etc/sysconfig/selinux .
  Comment this line
  
  • #SELINUX=enforcing
    and add this one
    
  • SELINUX=disabled
    
  • 
    I have to check the httpd.conf from linux. Otherwise:
    
    
  • Change the TimeOUT value to 3600 from 300
    
  • Change KeepALive to true
    
  • Change Listen 80 to Listen 0.0.0.0:80
    
  • Uncomment Include conf.d/*.conf
    
  • Add line 283 Allow from all
    
  • Change line 310 from
    • Options Indexes FollowSymLinks
      to
    • Options Indexes Includes FollowSymLinks ExecCGI
    
    
  • • AllowOverride None
      to
    • AllowOverride all
    
    
  • comment out UserDir disable
    
  • Uncomment UserDir public_html
    
  • After line 359 in the <Directory /home/*/public_html>
    you can add these lines
    

    <Directory /home/*/public_html>
            Options +ExecCGI +Includes +FollowSymLinks
            #SymLinksIfOwnerMatch
            #AllowOverride AuthConfig Limit
            AllowOverride All
            RewriteEngine On
            RewriteRule \.pm$ - [gone]
            RewriteRule \.ini$ - [gone]
    </Directory>
    

    
    
  • Change line 390 from
    • DirectoryIndex index.html index.html.var
      to
    • DirectoryIndex index.php index.shtml index.html index.cgi index.html.var
    
    
  • Uncomment AddHandler cgi-script .cgi
    

Step 3:

• config.inc.php.CENTOS to config.inc.php

• Line 7:
  Replace "your name" by the user name hosting the est-pac. In my case it is $config['install_dir'] = '/home/user/yvan/public_html/est-pac/';
• Lines 12 and 13:
  Replace DB1 and/or delete DB2 by the name of your database, the username and the password shouldn't be modified as they are used by the scripts to connect the database
  
• Line 16:
  One can blast locally if the value of $config['blast_local'] = 1 if set to 0 Blast Job are send to NCBI.
• Line 22:
  Change the "db_name" by the name of the database you formatdb your self (see formatdb note). For example if you formatted two dbs, ecoli.nt and sts like This:
  formatdb -o T -p F -i ecoli.nt -n ecoli.nt
  formatdb -o T -p F -i sts -n sts
  Then this line will look like that: $config['blast_databases'] = array('sw/ncbi/db/ecoli.nt' , 'sw/ncbi/db/sts');

• First you have to give the folder data the correct user / group and permission combination. Type in Terminal:
  • sudo su
  • chown -R "your name" /Users/"your login name"/Sites/est-pac/data
  • chgrp -R apache /Users/"your login name"/Sites/est-pac/data
  • chmod 775 /Users/"your login name"/Sites/est-pac/data

• Executable
• Download from NCBI the BLASTALL programs. Look for the blast-x.x.xx-ppc32-macosx.tar.gz file.
• Put them in the est-pac/sw/ncbi/ directory, then untar them (just double click them!)
• Make sure that you put the content of the newly create directory (BlastX.x.x) into the est-pac/sw/ncbi/ directory and not in est-pac/sw/ncbi/BlastX.x.x/!

• Databases
• From NCBI download the database you are interested in, for example: ecoli.nt.gz
• Move the downloaded file in est-pac/sw/ncbi/db/
• In Terminal type
  • cd /Users/"your login name"/Sites/est-pac/sw/ncbi/db
  • ../bin/formatdb -o T -p F -i ecoli.nt -n ecoli.nt.
    Note: Use the -o T option only if the ID line (after>) is UNIQUE, otherwise don't use it
    This command is for a nucleotide db! If you want to formatdb proteinic sequences type formatdb -o T -p T -i ecoli.aa -n ecoli.aa
• The name after the -n option should be put in this line in the config.inc.php file.
• For the one interested this page could be interesting ....

• Download HMMER in est-pac/sw/hmmer/.
• Untar put them in the est-pac/sw/hmmer/ directory
• Make sure that you put the content of the newly create directory (hmmer-x.x.x) into the est-pac/sw/hmmer/ directory
• Download Pfam_ls into /Sites/est-pac/hmmer/db/ and untar it

• Download this already compiled version of ESTScan
• Unzip it in the est-pac/sw/ directory