Instructions for creating COGEME website

1: CREATING DATABASE IN MYSQL

a)Create a database in MySQL called Cogeme21

From the MySQL console:  create database Cogeme21;

Exit the console

b)The file Cogeme21.sql contains a dump of the whole database

Read this into database Cogeme21 as below:

mysql -p Cogeme21 < Cogeme21.sql


c) You need to grant select privileges to the database for the user nobody (from the MySQL console)

GRANT SELECT ON Cogeme21.* TO nobody@localhost IDENTIFIED BY 'webaccess';

(this assumes that the database is on the same computer as the web server if not,
you might need to add a second line changing nobody@localhost to nobody@'machinename'
or nobody@'%' for any machine)

2: WEB PAGE AND PERL SCRIPTS

a) Folder "htdocs" contains HTML pages, "cgi-bin" contains Perl scripts.

b) The folder "seq" contains sequence files and "images" contains the COGEME logo. They should both be placed inside the "htdocs" file when installed on the webserver.

c) Perl scripts assume that Perl compiler is located at "/usr/bin/perl",
if not all headers need to be changed.

d) Perl module DBI needs to be installed as well as driver DBD-Mysql.

e) blast.pl and blastest.pl perform BLAST searches. BLAST software can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/.
Latest version at time of writing is blast-2.2.26. BLAST executables need to be installed in a directory in the current PATH.
Do not install BLAST+ software.
The  blast.pl and blastest.pl scripts each create two temporary files in /var/www/tmp/.
Change this if necessary, whatever directory is used needs to have correct permissions set to allow file creation.


3: SEQUENCE FILES

Sequence files are in the "seq" directory.
In our setup the sequence files are in the directory /var/www/seq/. If you put these files in a different directory then "blast.pl" and "blastest.pl" as well as the webpage "sequence.html" need to be edited to reflect this.
Format each sequence file as a BLAST database as below:

formatdb -i seq.fas -p F

where seq.fas is the name of the sequence file

Darren Soanes 24/08/12 email:d.m.soanes@exeter.ac.uk