Please follow the instructions during the installation carefully. +------------------------------------------------------------------------------------------------------------+ | UPDATE APACHE CONFIGURATION FILE (HTTPD.CONF) | +------------------------------------------------------------------------------------------------------------+ 1) Please open the httpd.conf file and add the following code: ### Manatee Environment Variables setenv WEBSERVER_TMP "/tmp" ### CGI access permissions to the /tmp area Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all ### Aliases ScriptAlias /tigr-scripts/ "/export/httpd/cgi-bin/" Alias /webserver_tmp/ "/tmp/" +------------------------------------------------------------------------------------------------------------+ | MANATEE SOURCE INSTALLATION | +------------------------------------------------------------------------------------------------------------+ In your shell: 1) cd install_chado_source 2) perl Makefile.PL PREFIX=/path/to/manatee/installation - You need to have all the libraries and modules installed which are required for this installation. The installation checks the missing libraries and tries to install it by default. If the installation is unable to do that, you need to install the missing libraries manually. The installation will not proceed until you install all the required libraries and modules. 3) make - If you have done some manual installation for the libraries then run "make clean" before running the "make" command. 4) make install - Sometime you will get the "permissions denied" errors. In that case you need to run the command as "sudo make install". To run this command you either have the administrative privileges or you need to ask you system administrator to do this for you. +------------------------------------------------------------------------------------------------------------+ | MANATEE DATABASE INSTALLATION | +------------------------------------------------------------------------------------------------------------+ After you have installed the manatee source you need to install the databases. In your shell : 1) cd install_chado_databases 2) perl Makefile.PL PREFIX=/path/to/manatee/installation - The installation will ask you several options. Please read them carefully and provide the correct options as they are very important for the successful installation. - The options will be: * - 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: 3) make - If you have entered wrong options and you are re-doing the installation, then you have to run "make clean" before running the "make" command. 4) make install - Sometime you will get the "permissions denied" errors. In that case you need to run the command as "sudo make install". To run this command you either have the administrative privileges or you need to ask you system administrator to do this for you. +------------------------------------------------------------------------------------------------------------+ | UPDATE MANATEE CONFIGURATION FILE (MANATEE.CONF) | +------------------------------------------------------------------------------------------------------------+ 1) Please update the "Manatee.conf" file to add the locations of the lookup files. 2) In you shell: [SHELL]$ emacs chado_prok_manatee/conf/Manatee.conf 3) In Manatee.conf file: 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 ************************************************************************************************************** * EXAMPLES * ************************************************************************************************************** +------------------------------------------------------------------------------------------------------------+ | MANATEE SOURCE INSTALLATION EXAMPLE | +------------------------------------------------------------------------------------------------------------+ [SHELL]$ sudo perl Makefile.PL PREFIX=/Library/WebServer/CGI-Executables/ CGI: found. DBI: found. XML::Parser: found. XML::Simple: found. XML::Writer: found. XML::Twig: found. Tree::DAG_Node: found. File::Spec: found. GD: found. GD::Text: found. GD::Graph: found. Storable: found. Date::Manip: found. IO::Tee: found. MLDBM: found. Log::Log4perl: found. DBD::mysql: found. HTML::Template: found. Log::Cabin: found. PREFIX is no longer a variable used for versions of ExtUtils::MakeMaker > 6.30. This variable will be renamed to INSTALL_BASE. The installation requires you to enter the PATH for your perl. You can know the path by typing "which perl" in the terminal window. Please enter the path here : /usr/bin/perl Please enter where your cgi executables should go:/Library/WebServer/CGI-Executables/ Please enter the apache DOCUMENTS :/Library/WebServer/Documents Checking if your kit is complete... Looks good Writing Makefile for Manatee [SHELL]$ make [SHELL]$ sudo make install Password: ....Cleaning the previous Manatee installtion ....Installing CGI scripts to /Library/WebServer/CGI-Executables/ ....Installing content files to /Library/WebServer/Documents [SHELL]$ +------------------------------------------------------------------------------------------------------------+ | MANATEE DATABASE INSTALLATION EXAMPLE | +------------------------------------------------------------------------------------------------------------+ [SHELL]$ perl Makefile.PL PREFIX=/usr/local/apache2 Added to MANIFEST: lookup_files/coding_hmm.lib.db.gz Added to MANIFEST: lookup_files/ec2go.db.gz Added to MANIFEST: lookup_files/hmm_go.db.gz Added to MANIFEST: lookup_files/pfam2role.db.gz Added to MANIFEST: lookup_files/prosite.db.gz Added to MANIFEST: lookup_files/role_data.db.gz Added to MANIFEST: lookup_files/tchar.db.gz Added to MANIFEST: lookup_files/tigrfam2role.db.gz Added to MANIFEST: Makefile.PL Added to MANIFEST: Manatee_database_installation.txt Added to MANIFEST: MANIFEST Added to MANIFEST: mysql/cgsp.ddl.gz Added to MANIFEST: perform_analyze_or_check_database.pl Please enter where do you want to store mysql_data:/usr/local/mysql/mysql/mysql_data/ Please enter the mysql USERNAME :usrABC Please enter the mysql PASSWORD :pwdXYZ Please enter the mysql SERVER/HOST name :USER-host.server.edu Please enter the directory where you want to store the LOOKUP FILES :/usr/local/apache2/databases/lookup_files/ You already have cgsp database in your mysql. - Please enter "Y" if you want to backup the existing cgsp database and install the new cgsp database. - Please enter "K" if you want to leave the existing cgsp database as it is. - Please enter "N" if you want to install a new copy of cgsp database Please enter your option here :N Writing Makefile for Manatee [SHELL]$ make Manifying blib/man3/perform_analyze_or_check_database.3pm [SHELL]$sudo make install Password: ....Copying mysql databases to /export/mysql/mysql/mysql_data/ ....Installing cgsp test database (this may take a while)... ....Performing "ANALYZE" on the databases (this may take a while)... Performing "Analyze" on the database "cgsp"... Done !!! [SHELL]$