README

Please see the manuscript by Langille et al. in Plos One: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010071

####Dependencies####

Assuming site is being installed on a standard LAMP (Linux Apache MySQL PHP) machine, the only other modules needed are:
php5-gd
sendmail

####Install####

*Insert ALL sql files (in the SQL folder) into MySQL starting with tb.sql first.

*Copy template files and enter your settings

*Move "include/secrets.php.sample" to "include/secrets.php" and edit:
 %%USER%%
  MySQL user with access to database
 %%PASS%%
  Password of MySQL user
 %%HOST%%
  Database server host, if unsure use: localhost
 %%DB%%
  Name of the database

*Move "include/config.php.sample" to "include/config.php" and edit:
 %%BASEURL%%
  The URL of the website where this code is installed. For example: http://www.biotorrents.com

*Visit the website and sign up for an account


###Installation Script###

A script to set up a new website. It will create the secret.php and config.php files with user supplied values. Then perform initial database import.

*Warning: Do not run on existing site

*Requirement: First create the MySQL database

*Change to scripts directory
 cd scripts
 
*Run install.php using your desired settings

*Command line options
 php install.php --user=USER --pass=PASS --db=DATABASE --host=HOSTNAME --baseurl=URL
 
*Replace USER and PASS with the MySQL user and password, DATABASE with the name of the MySQL database, and optionally the HOSTNAME of the MySQL server if other than localhost.
 
For example:
 --baseurl=http://www.biotorrents.net

*Visit the website and sign up for an account

*Values will be loaded from secrets.php and config.php they already exist