Where Oracle is used in the Lab

Oracle databases are used to manage sequencing and analysis activities in the Nickerson Lab. These databases are manipulated via a collection of command-line PERL scripts (eg. pAnalysis.pl) and a Java application for analysis (VG2), as well as the Java Servlet, web-based PGABench for laboratory workflow tracking.

Presently, there are 5 instances of Oracle in use:

Starting Oracle

  1. Login to database server.
  2. Become 'oracle' user. (eg. 'sudo su - oracle')
  3. Set ORACLE_SID environtment variable to the name of the database to be started. (eg. 'setenv ORACLE_SID pgatmp', where 'pgatmp' is the name of the database)
  4. Start svrmgrl console. (eg. 'svrmgrl')
  5. Login as sysdba. (eg. 'connect internal as sysdba')
  6. Issue command 'startup mount' command. (eg. 'startup mount pgatmp', where 'pgatmp' is the name of database)
  7. If mount successful, open access to users. (eg. 'alter database open')
  8. Quit svrmgrl program. (eg. 'quit')
  9. Quit 'oracle' shell. (eg. 'exit')

Stopping Oracle

  1. Login to database server.
  2. Become 'oracle' user. (eg. 'sudo su - oracle')
  3. Set ORACLE_SID environtment variable to the name of the database to be stopped. (eg. 'setenv ORACLE_SID pgatmp', where 'pgatmp' is the name of the database to be stopped)
  4. Start svrmgrl console. (eg. 'svrmgrl')
  5. Login as sysdba. (eg. 'connect internal as sysdba')
  6. Issue command 'shutdown immediate' command. This will disconnect all users and halt the database. This action can take quite a while. If this does not work, try 'shutdown abort'. This will result in the loss of data for any open transactions. You will need to restore the database using the archive logs.
  7. Quit svrmgrl program. (eg. 'quit')
  8. Quit 'oracle' shell. (eg. 'exit')

Fixing Oracle