Design Specs: Configuration setup and 3rd party software install

configuration

in wormbase.conf

turn the timing&caching information on

timer = 1 

when people submit/update issues, email alters will be sent out from this address

issue_email = oicr@wormbase.org 

email account when people register at WormBase

register_email = oicr@wormbase.org

email account for error reporting!

 <Plugin::ErrorCatcher::Email>
   to      oicr@wormbase.org   
   from    oicr@wormbase.org 
   use_tags 1
 #  subject Error Report from: %h; %F, line %l
 </Plugin::ErrorCatcher::Email>

wormbase user database configuration

<Model::Schema>
  schema_class = WormBase::Schema
  <connect_info>  
       dsn =  dbi:mysql:wormbase_user:hostname=...
       user = ..
       password = ..
   </connect_info>
</Model::Schema>

third party software

CutyCapt

this is used to provide pdf print function on the new site

http://cutycapt.sourceforge.net/

installation

 % sudo apt-get install subversion libqt4-webkit libqt4-dev g++
 % svn co https://cutycapt.svn.sourceforge.net/svnroot/cutycapt
 % cd cutycapt/CutyCapt
 % qmake
 % make

configure path to the executable

 <Model::WormBaseAPI>
   ...
   
     <print>
	  PRO_EXEC = ./CutyCapt
	</print>
   ...
  </Model::WormBaseAPI>

Blast/Blat

configuration

  <blast_blat>
	    base =  /usr/local/wormbase/databases/
	    blast = /blast/
	    SCORE_KEY_IMAGE = score_key.png
	    HSP_GENOME_LINK_PART_LIMIT = 10
	    HSP_ALIGNMENT_IMAGE_LIMIT  = 10
	    BLAST_EXEC_DIR = /usr/local/wormbase/services/blast
	    BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient
	    b_genome = c_elegans  c_briggsae ...
	    b_protein = c_elegans  c_briggsae ...
	    b_gene = c_elegans ...
	    b_est = c_elegans ...
	    ARCHIVES = WS100 WS110...
  </blast_blat>

Aligner

need to installation GBrowse libraries in order for it to work!

on dev, it's under

/usr/local/wormbase/website/staging/extlib/gbrowse2/current/lib/perl5/x86_64-linux-gnu-thread-multi/