Running joinerCheck for all databases: Difference between revisions

From genomewiki
Jump to navigationJump to search
(moving this from the static qa page docs)
 
(Replacing page with 'This page is no longer maintained.')
 
(3 intermediate revisions by one other user not shown)
Line 1: Line 1:
== Overview ==
This page is no longer maintained.
The joinerCheck program is run bi-monthly on all active databases on the hgwbeta machine. Errors that are found may be newly introduced or pre-existing. Corrections to data and/or all.joiner rules that impact browser users are given priority; corrections to known errors are made as time permits.
 
* When/Who: Run bi-monthly by a member of QA
* Why: Catch global rule problems with all.joiner or new data problems within assemblies
* Where: hgwbeta:/hive/groups/qa/joinerCheck
* Remember: Before starting, be sure to update your source tree so that you have the latest version of all.joiner
 
== Run joinerCheck -keys ==
 
* Create new directory at: /hive/groups/qa/joinerCheck/keys/YYYYMM
* In the past it has been useful to run against all DBs in three batches: (1) human, (2) mouse and rat, and (3) the rest. One batch per day, for three days in a row
* The goal is to have each DB run without conflicting with genbank updates. Never run overnight on a Sunday (EST updates). In the past, running Mon-Tue-Wed has been successful, starting in the morning after the previous night's genbank update has finished (~8am) and ending the batch before the next night's genbank updates start (~12pm)
* Execute Keys program hgwbeta:/hive/groups/qa/joinerCheck/keys/YYYYMM> nice nohup joinerBatchKeys.csh [hg | mm_rn | other | extra] &
* When the script finished, it sends an email to whoever ran it.
* When complete, execute Error program> getJoinerKeyErrors.pl /hive/groups/qa/joinerCheck/keys/YYYYMM
 
== Evaluate -keys result ==
* Create working directory to investigate problems at: /hive/groups/qa/joinerCheck/rules/YYYYMM
* Review results of getJoinerKeyErrors.pl summary report
* Compare to the last results to find out what is known, what is new, and what has been fixed since the last run
* Analysis hints:
** Review makedocs and all.joiner for tracks/assemblies with issues
** Attempt to isolate exact problem. Is it data or a rule problem?
** Original developer can help confirm track problems
** If it is a genbank table, confirm that genbank updates are on then contact Mark Diekhans
** Data fixes can often be made by QA, rule fixes are usually made by a developer
 
== Run joinerCheck -times ==
* Create new directory at: /hive/groups/qa/joinerCheck/times/YYYYMM
* Execute Times program hgwbeta:/hive/groups/qa/joinerCheck/keys/YYYYMM> nice nohup joinerBatchTimes.csh [hg | mm_rn | other | extra] &
 
== Evaluate -times result ==
* Use -keys working directory to investigate problems at: /hive/groups/qa/joinerCheck/rules/YYYYMM
* Review results
* Compare to the last results to find out what is known, what is new, and what has been fixed since the last run
* Analysis hints:
** Any and all output is considered an error
** Priority of found errors can be high if they involve proteome/known genes data
** Makedoc notes are the primary source for tracking changes
** Analysis hints from -keys analysis can be helpful for isolating root cause of -times errors, too

Latest revision as of 19:24, 10 March 2011

This page is no longer maintained.