Manatee Installation Below are the instructions for a full Manatee install. Please follow along from top to bottom and the installation will be much easier. Note: Please read over the README very carefuly to attain valuable and necessary configuration changes that will be required for Manatee to work with them.
The README files are platform specific.


Update the APACHE configuration file

• Please update the "httpd.conf" file and add the following code:


[SHELL]$ emacs httpd.conf








### Manatee Environment Variables
setenv WEBSERVER_TMP "/tmp"

### CGI access permissions to the /tmp area
< Directory "/tmp" >
    Options Indexes FollowSymLinks
    AllowOverride None
    Order allow,deny
    Allow from all
< /Directory >

### Aliases
< IfModule alias_module >
    ScriptAlias /tigr-scripts/ "/export/httpd/cgi-bin/"
    Alias /webserver_tmp/ "/tmp"
< /IfModule >



[SHELL]$

• For MAC OSX users: Please change folder name "/tmp" to "/private/tmp".

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Manatee Source Installation

• Download the latest Manatee source tarball.
• Please read the README file in the source for customizing your own installation.




SHELL> tar -xzvf manatee-x.x.x.tgz
SHELL> cd manatee/install_chado_cource
SHELL> perl Makefile.PL PREFIX=/path/to/manatee/installation
SHELL> make
SHELL> make install



• Click Here to see a sample installation.

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Manatee Standard Database Installation

• After you have installed the manatee source you need to install the databases.
  There are two types of required databases that Manatee needs,
  1. Project databases (CGSP), and
  2. Lookup file database.
  NOTE: The installation will ask you several choices to enter. Please read them carefully and complete them for a successful installation.


• To install the databases, please follow the instruction below:
  
  
  
  SHELL> cd manatee/install_chado_databases
  
  SHELL> perl Makefile.PL PREFIX=/path/to/manatee/installation
  Please enter where do you want to store mysql_data:/path/to/mysql_data
  Please enter the mysql USERNAME : username
  Please enter the mysql PASSWORD : user_password
  Please enter the mysql SERVER/HOST name :mysqlHOST
  Please enter the directory where you want to store the LOOKUP FILES :/path/to/store/lookup_files
  
  • If the installation doesn`t detect the presence of any current instance of CGSP database on the computer, it will directly going to install the database.
  • If the installation detects the CGSP database on the computer then you have to chose one of the three options the installation gives:
    1. Please enter "Y" if you want to backup the existing cgsp database and install the new cgsp database.
    2. Please enter "K" if you want to leave the existing cgsp database as it is.
    3. Please enter "N" if you want to install a new copy of cgsp database.
  • Please enter your option:
  
  
  SHELL> make
  
  SHELL> make install
  
  
  
• Click Here to see a sample installation.

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Update the configuration file

• Please update the "Manatee.conf" file to add the locations of the lookup files.




SHELL> emacs chado_prok_manatee/conf/Manatee.conf









• Prok:Mysql:localhost
  Chado:Mysql:localhost
  


• HMM_LOOKUP_FILE=path/to/lookup_files/coding_hmm.lib.db
  HMM_GO_LOOKUP_FILE=path/to/lookup_files/hmm_go.db
  TCHAR_LOOKUP_FILE=path/to/lookup_files/tchar.db
  PROSITE_LOOKUP_FILE=path/to/lookup_files/prosite.db
  EC2GO_LOOKUP_FILE=path/to/lookup_files/ec2go.db
  ROLES_LOOKUP_FILE=path/to/lookup_files/role_data.db
  
  

[SHELL]$

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