QA scripts

This is a list of the most frequently-used programs and scripts that QAers use. It does not include track-specific programs, such as chainNetTrio.csh. Some are devised by QA and live in the source tree at kent/src/utils/qa. Some are

Must know about!

bigPush.csh

Pushes tables in list to mysqlbeta and records size.

 Requires sudo access to mypush to run.
 
 Do not redirect output or run in the background,
 as it will require you to type your password in.
 Program will ask you for your password again after
 large tables. If you take too long to re-type in
 the table the script stalled on might not get
 pushed. Double-check that all tables have been
 pushed!
 
 Will report total size of push and write two files:
 db.tables.push -> output for all tables from mypush
 db.tables.pushSize -> size of push

commTrio.csh

Sorts and compares two files.  
Counts unique and common records.

    usage:  leftFileName rightFileName [rm]
            optional [rm]: remove the three output files when finished

compareWholeColumn.csh

 gets a column from a table on dev and beta and checks diffs.
 reports numbers of rows unique to each and common.
 can compare to older database.
 writes files of everything.

   usage:  database table column [db2] 

compareWholeTable.csh

 gets an entire table from two machines and checks diffs.
 reports numbers of rows unique to each and common.
 writes files of everything.
 not real-time on RR -- uses genome-mysql.

   usage:  database table [machine1] [machine2]
     (defaults to dev and beta)

Might also like!

checkPushedFiles.csh

checks to see if files are in place, after a push

usage: website files(s)

website should include the path of the directory where
the files reside, such as:
  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/ 

file(s) is either a single name or a list of names, and can
include items with additional directory structure, like so:
  filename
  dir/filename
  dir/dir/dir/filename

any output other than '200 OK' indicates an error.

compareTableToFile.csh

Ensures that a table correlates with its associated file.
Only prints results if there is a diff between table and file.
Works for these file types: narrowPeak, broadPeak, gappedPeak,
                            bedGraph, NRE, BiP, gcf
For wiggle files, you must specify [wig] parameter.

 usage:  database tableName fileName [wig] [verbose]
  fileName includes path of download file 
  e.g. /goldenPath/<db>/fileName.gz

  use verbose for more details