cd Notes installing the SBEAMS - BioLink module $Id$ ------------------------------------------------------------------------------- 1) Software Dependencies You must first install the SBEAMS Core. See the separate installation notes (sbeams.installnotes) on how to accomplish that. ------------------------------------------------------------------------------- 2) Installation Location SBEAMS is designed to live entirely in the "htdocs" area of your Apache web server. For the remainder of this installation, it will be assumed that your installation is configured as follows; compensate for your specific setup: servername: db DocumentRoot: /local/www/html Primary location: directly located in DocumentRoot, /local/www/html/sbeams --> http:/db/sbeams/ Development location: In a dev1 tree starting in the DocumentRoot, /local/www/html/dev1/sbeams -> http:/db/dev1/sbeams/ All modules live in the same area and should be unpacked into the main SBEAMS area. ------------------------------------------------------------------------------- 3) Create and populate the database It is assumed that you have already created and tested your SBEAMS Core database. You may either create a separate database for the BioLink database or you can put everything in the same database. Note that some database engines (rare now) may not permit cross-database queries in which case your may NOT use separate databases. If you do use separate databases, you may not be able to enforce referential integrety between tables in the different databases. This may or may not be a significant concern. - If you decide on a separate database, create it and within it, enable users "sbeams", "sbeamsro", "sbeamsadmin" as done for the Core. - Create directory to store BioLink sql statement files: cd $SBEAMS/lib/ mkdir sql/BioLink - Generate the appropriate schema for your type(s) of database as follows: set DBTYPE="mssql" #### one of mssql mysql pgsql oracle etc. cd scripts/Core/ ./generate_schema.pl \ --table_prop ../../conf/BioLink/BioLink_table_property.txt \ --table_col ../../conf/BioLink/BioLink_table_column.txt \ --schema_file ../../sql/BioLink/BioLink --module BioLink \ --destination_type $DBTYPE - Verify that the SQL CREATE and DROP statements have been correctly generated in $SBEAMS/lib/sql/BioLink/ cd $SBEAMS/lib/sql/BioLink more BioLink_CREATETABLES.mssql - Create all tables and constraints as described in the Core installnotes, e.g. $SBEAMS/lib/scripts/Core/runsql.pl -s BioLink_CREATETABLES.mssql -u sbeamsadmin $SBEAMS/lib/scripts/Core/runsql.pl -s BioLink_CREATECONSTRAINTS.mssql -u sbeamsadmin ##### MySQL ############### # # Execute these commands instead of the ones given above for MS SQL: # # $SBEAMS/lib/scripts/Core/runsql.pl -s BioLink_CREATETABLES.$DBTYPE -u sbeamsadmin --delimiter semicolon # $SBEAMS/lib/scripts/Core/runsql.pl -s BioLink_CREATECONSTRAINTS.$DBTYPE -u sbeamsadmin --delimiter semicolon # ########################### As explained in the sbeams.installnotes, you may also give runsql.pl a password on the command line if you so choose, otherwise you will be prompted for one. Examples for table creation for other database flavors can be found in the Core installation notes and will not be repeated here. ------------------------------------------------------------------------------- 4) Edit the SBEAMS Configuration files setenv SBEAMS /local/www/html/dev1/sbeams cd $SBEAMS/lib/conf edit SBEAMS.conf Specifically, change: DBPREFIX{BioLink} = BioLink.dbo. to the database name and schema/owner to prefix to table names. If your installation will have only one backend database, this will be the same prefix as you specified for the DBPREFIX{Core}. Add the BioLink module to available modules: $SBEAMS/lib/scripts/Core/addModule.pl BioLink ------------------------------------------------------------------------------- 5) Populate the driver tables cd $SBEAMS/lib/conf/BioLink ../../scripts/Core/update_driver_tables.pl BioLink_table_property.txt ../../scripts/Core/update_driver_tables.pl BioLink_table_column.txt If this doesn't work. Do not proceed, debug first. Now that the BioLink driver tables are loaded, you should be able to go to the web site again and click on SBEAMS - BioLink and explore the tables. They're all going to be empty, but you shouldn't get any errors, just empty resultsets. If this doesn't work. Do not proceed, debug first. NOTE: You will potentially need to re-run this step every time either of these files is updated (BioLink_table_property.txt and _column.txt) ------------------------------------------------------------------------------- 6) Populate some of the tables with initial data cd ../../refdata/BioLink - Load data into polymer_type table: ../../scripts/Core/DataImport.pl -s polymer_type.xml - Load data into work_group/table_group_security tables: ../../scripts/Core/DataImport.pl -s BioLink_work_groups.xml - Load data into the MGED ontology tables ../../scripts/Core/DataImport.pl --ignore_pK -s MGED_ontolgy_tables.xml - Load data into the dbxref table: ../../scripts/Core/DataImport.pl -s dbxref.xml ------------------------------------------------------------------------------ 7) You should now see a link for BioLink in the webUI (may require that you log back in). In order to use some of the administrative features you will have to add yourself to one or more of the work_groups that you created in the second command in the previous section, most importantly BioLink_admin. With your browser, navigate to: [SBEAMS Home] [Admin] [Manage User Group Associations], [Add ...], and add yourself (and appropriate others) to these groups. You are now ready to install any of the specific modules! ------------------------------------------------------------------------------- 8) Install Optional Modules While not required to run SBEAMS, the Gene Ontology module provides a very convenient way to view Gene Ontology Annotations (GO) in some SBEAMS queries. Instructions can be found at: $SBEAMS/doc/BioLink/GeneOntology.installnotes You can always install this at a later time as well.