Instructions for fresh install of Django Based BioDIG Database. The example here is of the MyDIG Mycoplasma database that is implemented using BioDIG tools.

Prerequisites: (THIS IS THE HARDEST PART) Django - Web framework used for website -- https://docs.djangoproject.com/en/1.3/topics/install/

PostgreSQL - database system used for website -- aptitude install postgresql-8.4
			- for Django make sure that in pg_hba.conf that 

MySQL - database system used with a GO database clone

Apache - Web Server for Django -- aptitude install apache2

mod-wsgi - mod for Apache for Django -- aptitude install libapache2-mod-wsgi

GBrowse - genome browser used -- http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO (WATCH FOR PREREQUISITES)

Chado - database schema used for organism database 
        -- http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/INSTALL.Chado (You may only need the prerequisites with the dump)

SQLite - database used to back GBrowse 
	-- CPAN DBD::SQLite for adaptor
	-- aptitude install sqlite3
	
Django files - the package (files) in order to create the website

BioPerl - http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

Pip - aptitude install python-pip

Sorl-thumbnail - pip install sorl-thumbnail

BioPython - aptitude install python-biopython

GFFParser - go to this page: http://biopython.org/wiki/GFF_Parsing
	and make sure that the link below is still valid
	-- go to: http://github.com/chapmanb/bcbb/
	-- download the source here as a zip file
	-- unzip this file and in the gff directory run:
		sudo python setup.py install

Instructions:

1. Clone git repository into /var/www/

2. Change name of folder from MyDIG to mycoplasma_site

3. Change the owner of this folder (recursively) to : Change the owner of /etc/gbrowse2 (recursively) to :

4. Replace the GBrowse.conf in /etc/gbrowse2 with the GBrowse.conf in the configuration folder Also, move the mycoplasmaTemplate.conf file into the /etc/gbrowse2 folder

5. Add Alias to apache2.conf (or httpd.conf) file -typically located in /etc/apache2/ -command: WSGIScriptAlias / /var/www/mycoplasma_site/apache/django.wsgi

6. Create a user for the psql databases with username/passwords given in settings.py and grant all privileges to this user on the databases

7. Create the same user in MySQL. Clone the GO database at http://www.geneontology.org/GO.downloads.ontology.shtml. get the database dump for MySQL that is updated daily

8. Once all databases created, in /var/www/mycoplasma_site/ run: python manage.py syncdb

9. Alter the table "organism" in the chado database using the statement: ALTER TABLE organism DROP CONSTRAINT "organism_c1". Otherwise, the database will not allow the same species in value in the species column, which we need.

10. Make sure there is a value in chado in the db table: there should be an entry with db_id=41, name=_global. Also make sure that there is a /var/www/mycoplasma_site/mycoplasma_home/genomeFiles/current folder and a /var/www/mycoplasma_site/mycoplasma_home/genomeFiles/new folder. Then run databaseUpdater/GenomeDB/GenomeUpdater.py

*11. Test to see what is working: If GBrowse is not working check your machine's URL for GBrowse then go into /var/www/mycoplasma_site/mycoplasma_home/templates/public/gbrowse.html and replace the iframe src with that URL

12. In your terminal, move to the directory /var/www/mycoplasma_site/databaseUpdater. Run the following command: python GenomeUpdater.py

13. Add the cron job for pruning to crontab to run every Saturday at 3:00am (should already be configured in the cron tab sh for pruning)