Notes add a new module:

#### Set this to the full name of the new module
set DEST = Genotyping

#### Set this to a unique two-letter code for the new module.
#### Do not duplicate existing two-letter codes. Code may be
#### longer than two letters, but not recommended.
set TAG = GT

--

#### DO NOT CHANGE THIS
set TEMPLATE = MODULETEMPLATE
set TMPLTAG = ModTmpTAG

---

cd /net/dblocal/www/html/dev2/sbeams/lib/perl/SBEAMS
#rm -r ${DEST} ${DEST}.pm
cp -p $TEMPLATE.pm $DEST.pm
cp -p -r $TEMPLATE $DEST
replaceall.pl $TEMPLATE $DEST $DEST.pm
cd $DEST
replaceall.pl $TEMPLATE $DEST *.pm
replaceall.pl ${TMPLTAG}_ ${TAG}_ *.pm
rm -r CVS .svn

---

cd /net/dblocal/www/html/dev2/sbeams/cgi
#rm -r ${DEST}
cp -p -r $TEMPLATE $DEST
cd $DEST
replaceall.pl $TEMPLATE $DEST *.cgi
replaceall.pl sbeams$TMPLTAG sbeams$TAG *.cgi
replaceall.pl ${TMPLTAG}_ ${TAG}_ *.cgi
rm -r CVS .svn

---

cd /net/dblocal/www/html/dev2/sbeams/lib/conf/Core
ed Modules.conf and/or AvailableModules.conf to include new module

cd /net/dblocal/www/html/dev2/sbeams/lib/perl/SBEAMS/Connection
ed TableInfo.pm to add link to new module at top

---

cd /net/dblocal/www/html/dev2/sbeams/lib/perl/SBEAMS/$DEST
ed TableInfo.pm
ed Tables.pm
  to add some initial tables
ed HTMLPrinter.pm
  to add links to manageable tables

cd /net/dblocal/www/html/dev2/sbeams/lib/conf
ed SBEAMS.conf
ed SBEAMS.conf.template
  to add database location definitions for new module
DBPREFIX{Genotyping}    = sbeams.dbo.

---

This would a be good time to create a new database if the module
calls for it, given r/w access to the sbeams user and r/o to sbeamsro.

cd /net/dblocal/www/html/dev2/sbeams/lib/conf
#rm -r $DEST
mkdir $DEST
cd $DEST
cp -p ../${TEMPLATE}/${TEMPLATE}_table_property.txt ${DEST}_table_property.txt
cp -p ../${TEMPLATE}/${TEMPLATE}_table_column.txt ${DEST}_table_column.txt
replaceall.pl ${TMPLTAG}_ ${TAG}_ *
replaceall.pl $TEMPLATE $DEST *
  edit them to reflect desired tables

---

Create the DDL files and create the tables in the database

cd /net/dblocal/www/html/dev2/sbeams/lib/scripts/Core
setenv MODULE $DEST
if ( ! -d "../../sql/$MODULE") mkdir ../../sql/$MODULE
./generate_schema.pl --table_prop ../../conf/$MODULE/${MODULE}_table_property.txt --table_col ../../conf/$MODULE/${MODULE}_table_column.txt --schema_file ../../sql/$MODULE/$MODULE --destination_type mssql

See section 5 of the sbeams.installnotes for details on how
to create the database objects with the resulting files in
/net/dblocal/www/html/dev2/sbeams/lib/sql/$DEST

---

Load those tables into the database if desired
cd /net/dblocal/www/html/dev2/sbeams/lib/scripts/Core
ed batch_update_driver_tables.pl
  (Add two lines for new driver tables and run the additions)
set CONFDIR = "../../conf"
./update_driver_tables.pl $CONFDIR/${DEST}/${DEST}_table_property.txt
./update_driver_tables.pl $CONFDIR/${DEST}/${DEST}_table_column.txt

---

Add in user groups like ${DEST}_admin, ${DEST}_user, ${DEST}_readonly if desired.
Make some users belong to these groups

Create table_group_security entries for these groups and the
table groups defined in ${DEST}_table_property.txt

Create table_group_security entries for new groups for common and rowprivate

---

Add the scripts directory and add load_biosequence_set support if desired:

cd /net/dblocal/www/html/dev2/sbeams/lib/scripts
mkdir $DEST
cd $DEST
ln -s ../share/load_biosequence_set.pl
cd ../share
ed load_biosequence_set.pl
cd ../Core
ed UpdateSymLinks.pl


---

Add query_option data:

cd /net/dblocal/www/html/dev2/sbeams/lib/sql/$DEST
cp -p ../ProteinStructure/ProteinStructure_POPULATE.mssql ${DEST}_POPULATE.mssql
ed ${DEST}_POPULATE.mssql
execute


---
Test in your dev2 area.  Once all is good, check into CVS or Subversion:


cd /net/dblocal/www/html/dev2/sbeams/cgi
cd $DEST
pur
cd ..
cvs add $DEST
cvs add $DEST/*

cd /net/dblocal/www/html/dev2/sbeams/lib/perl/SBEAMS
cd $DEST
pur
cd ..
cvs add $DEST.pm
cvs add $DEST
cvs add $DEST/*

#cd /net/dblocal/www/html/dev2/sbeams/images
#cvs add -kb biosap_logo.png

cd /net/dblocal/www/html/dev2/sbeams/lib/conf
cd $DEST
pur
cd ..
cvs add $DEST
cvs add $DEST/*

cd /net/dblocal/www/html/dev2/sbeams
cvs commit


Added new Genotyping Module