version 0.953  Monday May 18,2009

This initial release is unfortunately with minimal documentation.
Future releases will be better documented.

The EdgeExpressDB (eeDB) system is a perl/mysql/web cgi system
with AJAX javascript clients.  
We recommend installing on linux, FreeBSD, or OpenBSD systems.
In order to have the full system installed one will need the following.

1) install Mysql 4.x or 5.0.x database server(s)

2) install http server(s) (apache2 recommended)
   with both CGI and FastCGI enabled
   the CGI and FastCGI must be configued so that it works
   with scripts ending in .cgi and .fcgi since the eeDB system
   automatically creates new web-service directories for each
   new eeDB instance.

3) install the EEDB perl module system.  best to use
   either  
   cpan EEDB
   or
   perl Makefile.PL
   since there are dependancies on other cpan packages

4) install a copy of Bioperl. This was not included in 
   the CPAN dependencies. It is used by some subsystems

5) run the install.sh script.  this will create
   /usr/local/EdgeExpressDB and populate it with required
   support files and scripts.
   One should then add /usr/local/EdgeExpressDB/bin to
   the PATH environment variable.

6) configure the following environment variables for the super-user 
who will be creating new eeDB instances
declare -x EEDB_REGISTRY="mysql://<user>@mysql-host.local.domain/eeDB_registry"
declare -x EEDB_WEBDIR="/var/www/html/eeDB"  #or where your webserver keeps the htdoc files
declare -x EEDB_WEBROOT="http://my-webserver.local.domain/eeDB/"


This will provide you with the base install of the system.
One then needs to create "instances" of eeDB database.
One uses the eedb_create_instance.pl script to do this.

First one should create the eeDB_registry instance

eedb_create_instance.pl -url "mysql://<user>:<pass>@mysql-host.local.domain:3308/eeDB_registry"

and then create as many instances for data as needed
eedb_create_instance.pl -url "mysql://<user>:<pass>@mysql-host.local.domain:3308/eeDB_instance1"
eedb_create_instance.pl -url "mysql://<user>:<pass>@mysql-host.local.domain:3308/eeDB_brain_study"
eedb_create_instance.pl -url "mysql://<user>:<pass>@mysql-host.local.domain:3308/eeDB_public_data"


THEN one needs to load data.  There are several loader scripts already made and
available in /usr/local/EdgeExpressDB/scripts.  If one needs custom scripts
please one these as a template and modify for your custom file formats.
There is some test data available in /testdata.  One can also easily download
bed files from the UCSC table browser.

EXAMPLE loading
eedb_load_bed.pl -url "mysql://<user>:<pass>@mysql-host.local.domain/eeDB_public_data" -assembly hg18 -fsrc "gene::UCSC_hg18_refgene_test" -file testdata/hg18_refgene_2009jan15.bed.gz  -block -store

If everything was installed properly one should now be able to use a web browser to 
access any of these instances
  http://my-webserver.local.domain/eeDB/eeDB_public_data/contents
and see the new source UCSC_hg18_refgene_test listed
One should also be able to go to 
  http://my-webserver.local.domain/eeDB/eeDB_public_data/view
and search for  NM_001002294
and then see the gene appear in the search and be able to select it.

Other useful loader scripts include eedb_load_gff3.pl and eedb_load_expression_table.pl

===
this is the first public release of the system, please understand and contact the author.
For this first release we are primarily releasing for collaborators who we can work
more closely with to train on the system.  We hope this collaboration process will help
us refine the system and documentation.

--- 
Jessica Severin, RIKEN OSC
jessica.severin@gmail.com


