README

PLEASE ENSURE EVERYING IS WITHIN DIRECTORY CALLED rnavirusdb IN YOUR 
/library/webserver/documents AND THEN FOLLOW POINTS 1 TO 4 BELOW

** 1 ** Install mySQL (see http://www.mysql.com/)

** 2 ** Load Tthe MySQL database from enclosed dump with the following.
shell prompt: gunzip rnavirusdb_dump.gz
shell prompt: mysql -h HOSTNAME -u USERNAME -p DATABASENAME < rnavirusdb_dump
where HOSTNAME, USERNAME, and DATABSENAME are as specified in the 
config.php file (see below). This command will prompt you to enter the 
password, which you can also see in the config.php file.

** 3 ** Copy dummy-config.php as config.php and type the mySQL details that you
used to create your database, e.g.

define('DB_NAME', 'rnavirusdb');     // The name of the database
define('DB_USER', 'my_username');     // Your MySQL username
define('DB_PASSWORD', 'my_password'); // ...and password
define('DB_HOST', 'localhost'); // host name if not localhost

** 4 ** The rnavirusdb web site uses some external programs listed below with 
sources. Type the paths to these programs into config.php where indicated.

** 5 ** BlastAlign.cgi and BlastAlign2.cgi in cgi-bin must be copied to your 
CGI-Executables directory and made executable by all. Note the line near the
beginning of these scripts (clines 8-10) that must be edited to set $website_dir 
and $website_URL to the absolute path of the web site's rnavirusdb directory and
the URL of the application respectively.

** 6 ** Give all write plus execute permissions on rnavirusdb/tmp 

TreeGraph (tgf) tgf10rc4.zip
http://www.math.uni-bonn.de/people/jmueller/extra/treegraph/

ps2pdf is a script bundled with Ghostscript that converts PostScript input 
into a PDF document.
http://www.ghostscript.com/awki
pstopdf is a MacOSX Terminal command that does the same thing

clustalw
http://www.ebi.ac.uk/clustalw/
http://www.embl-heidelberg.de/~chenna/clustal/darwin/

BLAST 
http://www.ncbi.nlm.nih.gov/BLAST/

readseq
http://sourceforge.net/projects/readseq
http://bioinformatics.ubc.ca/resources/tools/readSeq
http://iubio.bio.indiana.edu/soft/molbio/readseq/

PAUP
http://paup.csit.fsu.edu/

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NOTICE

This product includes sofware developed by Robert Belshaw, Tulio de
Oliveira,Sidney Markowitz and Andrew Rambaut. Anyone contributing object code,
source code, patches, documentation, etc. certifies that it can be
redistributed under the same license terms and conditions as the
product itself.