Download the httpd-2.0.49.tar.gz file.
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Please read the INSTALL README file in the source for customizing your own installation.
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As Root User:
shell> tar -xzvf httpd-2.0.49.tar.gz
shell> cd httpd-2.0.49
shell> ./configure
shell> make
shell> make install
shell> /usr/local/apache2/bin/apachectl start
Edit Apache Configuration for Manatee:
1. Open the /usr/local/apache2/conf/httpd.conf file to make Manatee specific changes
2. At the top of the conf file (line 1), you must set a WEBSERVER_TMP environment variable:
setenv WEBSERVER_TMP /tmp
You may set the WEBSERVER_TMP location to anything you like, but be advised that if you don't set it to a location that automatically deletes older files, your system may run out of space quickly.
Also, some webserver installations use a different syntax than setenv. If SetEnv does not work, you may want to try the following. Please see the documentation for your installation for more specific information.
export WEBSERVER_TMP=/tmp
3. Under the ScriptAlias section, add the following lines:
ScriptAlias /tigr-scripts/ "/usr/local/apache2/cgi-bin/"
Alias /webserver_tmp "/tmp/"
There should already be a default ScriptAlias for cgi-bin which will look similar to the line below. Add the above lines under this.
ScriptAlias /cgi-bin/ "/usr/local/apache2/cgi-bin/"
4. Restart Apache:
shell> /usr/local/apache2/bin/apachectl restart
Download the Standards Linux (x86, libc6) MySQL 4.0.17 file.
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Please read the INSTALL-BINARY README file in the source for customizing your own installation.
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As Root User:
shell> /usr/sbin/groupadd mysql
shell> /usr/sbin/useradd -g mysql mysql
shell> cd /usr/local
shell> tar -xzvf mysql-standard-4.0.17-pc-linux-i686.tar.gz
shell> ln -s mysql-standard-4.0.17-pc-linux-i686 mysql
shell> cd mysql
shell> ./scripts/mysql_install_db
shell> chown -R root .
shell> chown -R mysql data
shell> chgrp -R mysql .
shell> bin/mysqld_safe --user=mysql &
Add MySQL Users/Passwords for Manatee:
shell> mysql --user=root mysql
mysql> DELETE FROM user WHERE User="";
Below, make sure you change "your_user_name" and "your_password" to the username and password you would like to use:
mysql> GRANT ALL ON *.* TO 'your_user_name' IDENTIFIED BY 'your_password' WITH GRANT OPTION
This query sets up a user called access which will have read-only privileges to the database:
mysql> GRANT SELECT ON *.* TO 'access' IDENTIFIED BY 'access' WITH GRANT OPTION
mysql> exit
shell> mysqladmin -u root reload
Click on the Download link above to see a list of required perl modules and their download locations.
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HTML::Template Bug: This perl module has a bug in it that causes it to fail in Manatee. Unfortunately, it seems no updates to this module will occur in the near future so it must be fixed manually. Please see below to fix your module or go to the Troubleshooting Page.
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Manual Fix of HTML::Template
This fix assumes that you have unpacked the HTML::Template in /usr/local/src. If you have removed it already after you installed it the first time, please download and unpack it again.
shell> cd /usr/local/src/HTML-Template-2.6
shell> emacs Template.pm
Place "use bytes;" at the top of the script next to the other "use" statements.
Then, go to line 1910 and change:
$which= uc($1); #which tag is it
to
$which = uc("$1"); #which tag is it
Save and close Template.pm. Now the module must be recompiled:
shell> perl Makefile.PL
shell> make
shell> make test
shell> make install
The bug should be fixed and you can move on to the next step.
Download the latest Manatee source tarball.
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Please read the INSTALL README file in the source for customizing your own installation.
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Solaris Users. In the Manatee source, please copy the configure.solaris version of the configure script to configure to install Manatee on Solaris properly:
shell> cp configure.solaris configure
Then follow the instructions below.
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As Root User:
shell> ./configure
There may be times where your installations of apache and mysql are not located in typical locations. There are several variables you can pass into the configure script to point to those locations. There are the variables:
APACHEBIN=/usr/local/apache2/bin
HTTPD=/usr/local/apache2/bin/httpd
MYSQLBIN=/usr/local/mysql/bin
MYSQLD=/usr/local/mysql/bin/mysqld
Here's an example of using these variables:
shell> ./configure APACHEBIN=/usr/local/apache2/bin HTTPD=/usr/local/apache2/bin/httpd MYSQLBIN=/usr/local/mysql/bin MYSQLD=/usr/local/mysql/bin/mysqld
shell> make
shell> make install
8. Manatee Standard Database Installations | Download
This tarball contains 2 required databases that Manatee will need to run all project databases, 1 demo project database, and 1 demo flat file database. Once installed, you will have a demo project database in which to test your Manatee installation. To install, please follow the instruction below:
Download the database installation tarball above to a location with a lot of space. The tarball contains the databases so it will take up a significant amount of disk space (482 Mb). For our purposes here, we will assume that we have downloaded it into /usr/local.
We will also assume that your MySQL data location is in /usr/local/mysql/data and that you do not have a search_data directory. The installation script will automatically make one for you in the path that you provide to the script below (unless it is already there). For our purposes, we will install the flat file search data into /usr/local/search_data
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Please read the README file after untarring the database installation tarball for a more detailed description of how to install the databases.
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As Root User:
shell> cd /usr/local
shell> tar -xzvf install_demo.tgz
shell> cd install_demo
shell> ./install_demo /usr/local/mysql/data /usr/local/search_data
Note that the install_demo script takes in two arguments. The first must be the MySQL data location and the second must be the location where you want the flat file databases to go.
9. Using Manatee for the First Time
Once everything above has been installed, you should be able to use Manatee with relative ease. The Manatee Source Installation step did the following. The CGI scripts and API were installed in a cgi-bin area designated by you in your httpd.conf file. Here, we will assume that the installation took place in /usr/local/apache2. Both prokaryotic and eukaryotic versions of Manatee were installed in the same locations and has affected only 2 locations on your filesystem.
CGI/API Source Code
/usr/local/apache2/cgi-bin will contain a euk_manatee and a prok_manatee directory
HTML/CSS Source Code
/usr/local/apache2/htdocs will contain a tdb directory which will contain a euk_manatee and a prok_manatee directory
Modifying the Manatee.conf File
The Manatee.conf file will be located in /var/www/cgi-bin/prok_manatee/conf. You must make sure that you modify the variables in this file to accomodate your system. Below are listed the variables that users typically have to change:
ANNOTATION_DIR - Change this to point to your "search_data" directory.
IPRSCAN_DIR - Change this to point to where you installed iprscan.
GZCAT - Change this to point to either gzcat OR zcat.
Accessing Manatee in your Browser
To access Manatee, you will go to a URL that will be like the following (depending on what organism type you are working with):
http://SERVER:PORT/tdb/prok_manatee
OR
http://SERVER:PORT/tdb/euk_manatee
In our example, I would access Manatee by going to:
http://localhost/tdb/prok_manatee/
And this page will redirect me to the login screen. At the login screen, put in your database user name and password that you set up in the MySQL Installation and enter in your database id. Database ids vary but will be much like the following:
gvc, gsp, etc. for prokaryotic organisms
ath1, pfa1, etc. for eukaryotic organisms
Troubleshooting
During very technical installations like this one, you are bound to run into problems. We will try and keep an up-to-date Troubleshooting page that may have answers to your questions.
User's Manual (coming soon)
Unfortunately, we do not have any user documentation beyond installation instructions and troubleshooting. We hope to have more in the future. Although we cannot offer a specific date for releasing new documentation, check back periodically for updates.
