[Gmod-schema-cmts] schema/chado README.Apollo,1.3,1.4

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31278

Modified Files:
	README.Apollo 
Log Message:
reworking the Apollo documenation


Index: README.Apollo
===================================================================
RCS file: /cvsroot/gmod/schema/chado/README.Apollo,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** README.Apollo	5 Mar 2005 11:34:33 -0000	1.3
--- README.Apollo	29 Apr 2005 18:07:58 -0000	1.4
***************
*** 7,15 ****
      meantime, you can grant all using sqlt and the template, 
      bin/privileges.tmpl 
!   - insert several ad hoc ontology terms found in 
!     modules/sequence/apollo-bridge/ontology_inserts.sql
    - insert a few misc items like those found in 
      modules/sequence/apollo-bridge/apollo.inserts
!     (heh! try to be a little more vague next time!) 
    - add the functions and triggers to chado.  Use the perl script:
        % /usr/local/bin/gmod_apollo_triggers.pl create
--- 7,34 ----
      meantime, you can grant all using sqlt and the template, 
      bin/privileges.tmpl 
! 
!     sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql <databasename>
! 
!     You can edit the template to grant privileges to just specific
!     users instead of PUBLIC.
! 
!   - insert several ad hoc cv terms found in 
!     modules/sequence/apollo-bridge/cv_inserts.sql. This file
!     contains sql commands to insert several controlled vocabulary terms
!     that Apollo expects to be in the database.  This file can be recreated
!     with additional terms as needed by editing the file
!     modules/sequence/apollo-bridge/ad_hoc_cv and running the perl script
!     modules/sequence/apollo-bridge/insert_ad_doc_cv.pl.  The resulting 
!     sql file can be inserted into the database with this command:
! 
!       $ psql $DBNAME <modules/sequence/apollo-bridge/cv_inserts.sql 
! 
    - insert a few misc items like those found in 
      modules/sequence/apollo-bridge/apollo.inserts
!     
!     Essentially, Apollo and chado have to agree about what the names
!     in the analysis table are, and there needs to be a few terms in 
!     the cv table. 
! 
    - add the functions and triggers to chado.  Use the perl script:
        % /usr/local/bin/gmod_apollo_triggers.pl create
***************
*** 18,20 ****
--- 37,45 ----
      the triggers for that. 
  
+ I understand that these directions are somewhat vague.  Getting Apollo to
+ work with chado requires a little hands on tinkering.  If you find yourself
+ having difficulties, please contact me.
  
+ Scott Cain
+ ca...@cs...
+ 4/29/05