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INSTALLATION AND CONFIGURATION OF THE EST2uni WEB SITE
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EST2uni is shipped with a web site with powerful data mining capabilities
oriented to the end user. This web site is provided as an example, but it
can be easily adapted and modified to your local needs.

Everything you need to set up the web site is in the directory 'php'. The
browseable web pages are located in the 'php/web_site' directory. The code
for these web pages has few lines of PHP; the main work is done by the code
located at the 'php/estpipe' directory.


WEB SITE INSTALLATION
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1.- Copy the contents of the 'php' directory to your Apache root directory:

	> cp -r php/* /var/www/

2.- Prepare the configuration file:

	> cd /var/www/est2uni/
	> cp configuration.php.example configuration.php

3.- Edit the configuration file to adapt it to your environment. The main parameters to
change are 'www_host', 'default_database', and 'apache_dir'.

4.- Copy your chromatograms in the directory indicated with the
'chromat_dir' parameter at the configuration file (one subdirectory per
library), in order to allow to retrieve them from the web page.

5.- Create MySQL accounts for your users. Every user should have the following
privileges:

	- SELECT and CREATE TEMPORARY TABLES on the EST database
	- INSERT and DELETE on the temp table.

As an example, if we want to create the user 'guest' with the password 'hello'
in the 'test' database at the host 'localhost', we just need to execute the
following statements:

	> mysql -u root -p
	Passwd:
	mysql> GRANT SELECT,CREATE TEMPORARY TABLES ON test.* TO 'guest'@'localhost' IDENTIFIED BY 'hello';
	mysql> GRANT INSERT,DELETE ON test.temp TO 'guest'@'localhost';

(NOTE: in order to grant these privileges, the database and the temp table
must already exist.)

(NOTE: this could also be done by a MySQL user with GRANT privileges on 'test'
database at localhost, other than root.)

6.- Be sure that Apache has writing permissions on 'est2uni/temp'
directory, and set the sticky bit to that directory:

	> cd /var/www/est2uni/
	> chmod 1777 temp

7.- Point your browser to http://localhost/est2uni/login.php and check that
everything is OK.

8.- Customizations can be easily done by changing the non-PHP HTML code of
the files at est2uni directory. Several independent EST projects can
be managed by setting up different est2uni directories with different
names. All of them will use the same PHP functions at estpipe directory.


WEB SITE BLAST SERVER SETUP
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Any BLAST-formatted database can be served, but we will assume in this example
that we want to set up the database with the unigenes obtained on the EST
pipeline analysis.

1.- Prepare the unigenes BLAST-formatted database. (There's a script in the 'utils'
directory that will do the trick.)

	> cd perl/utils/
	> reformat_db <host> <database> <mysql_user> <password> <output_file>

2.- Check that the number of sequences is OK:

	> cat <output_file> | grep -e '^>' | wc -l

3.- Check that the BLAST formatting was OK:

	> cat formatdb.log

4.- Move all the index files to the blast subdirectory under the est2uni
directory:

	> mv *.n* /var/www/est2uni/blast/

5.- Edit the 'blast.rc' and 'ncbi_blast.rc' files in 'php/estpipe/blast' directory.

6.- Set in the 'configuration.php' file the list of the databases on the
'blast_dbs' parameter.

7.- Check that the BLAST web server is working by running a BLAST search.