a048e0b385f2984b3de06c29fbe67807ec9ecdbb
mspeir
  Mon Mar 14 15:36:29 2016 -0700
Some updates to my autopushed track QA script. Added log file info to help message. Script now displays help message if it is run with no arguments. Added some checks to make sure important variables aren't empty. Changed how issue messages are generated. Link to log file is at bottom of list of issues found. Fixed some minor bugs including issue with bc not liking very small numbers and script not correctly reporting large coverage differences. Also added script to makefile. refs #12561

diff --git src/utils/qa/makefile src/utils/qa/makefile
index 5f6f3f4..1c37f87 100644
--- src/utils/qa/makefile
+++ src/utils/qa/makefile
@@ -1,140 +1,141 @@
 include ../../inc/common.mk
 # ${SCRIPTS} is ${HOME}/bin/scripts (defined in kent/src/inc/common.mk)
 # to install in /cluster/bin/scripts/, run (in this directory):
 # make SCRIPTS=/cluster/bin/scripts
 
 install:
 	@echo Reminder: is your sandbox up to date?
 	cp -p --remove-destination 2bitCompare             ${SCRIPTS}
 	cp -p --remove-destination activeGenbank.csh       ${SCRIPTS}
 	cp -p --remove-destination alertBqueue.csh         ${SCRIPTS}
 	cp -p --remove-destination allowTraffic.csh        ${SCRIPTS}
 	cp -p --remove-destination backupCentral.csh       ${SCRIPTS}
 	cp -p --remove-destination bamToBedGraph.csh       ${SCRIPTS}
 	cp -p --remove-destination bamToBigWig.csh         ${SCRIPTS}
 	cp -p --remove-destination bigPush.csh             ${SCRIPTS}
 	cp -p --remove-destination blatPing.csh            ${SCRIPTS}
 	cp -p --remove-destination browserUsage.csh        ${SCRIPTS}
 	cp -p --remove-destination catchBot.csh            ${SCRIPTS}
 	cp -p --remove-destination chain.csh               ${SCRIPTS}
 	cp -p --remove-destination chain2.csh              ${SCRIPTS}
 	cp -p --remove-destination chainNetTrio.csh        ${SCRIPTS}
 	cp -p --remove-destination checkAllStaticLinks.csh ${SCRIPTS}
 	cp -p --remove-destination checkBOT.csh            ${SCRIPTS}
 	cp -p --remove-destination checkCoverage.csh       ${SCRIPTS}
 	cp -p --remove-destination checkEncodeRegions.csh  ${SCRIPTS}
 	cp -p --remove-destination checkGbdbDiffs.csh      ${SCRIPTS}
 	cp -p --remove-destination checkGenomeMysql        ${SCRIPTS}
 	cp -p --remove-destination checkHitter.csh         ${SCRIPTS}
 	cp -p --remove-destination checkMachineName.csh    ${SCRIPTS}
 	cp -p --remove-destination checkMetaData.csh       ${SCRIPTS}
 	cp -p --remove-destination checkMetaAday.csh       ${SCRIPTS}
 	cp -p --remove-destination checkOffend.csh         ${SCRIPTS}
 	cp -p --remove-destination checkPushedFiles.csh    ${SCRIPTS}
 	cp -p --remove-destination checkScaffoldGaps.csh   ${SCRIPTS}
 	cp -p --remove-destination checkStaticLinks.csh    ${SCRIPTS}
 	cp -p --remove-destination checkStoreUnits.csh     ${SCRIPTS}
 	cp -p --remove-destination checkSync.csh           ${SCRIPTS}
 	cp -p --remove-destination checkSyncAll.csh        ${SCRIPTS}
 	cp -p --remove-destination checkTableStatus.csh    ${SCRIPTS}
 	cp -p --remove-destination checkTrackUiLinks.csh   ${SCRIPTS}
 	cp -p --remove-destination checkWigFiles.csh       ${SCRIPTS}
 	cp -p --remove-destination commTrio.csh            ${SCRIPTS}
 	cp -p --remove-destination compareHgFindSpecs.csh  ${SCRIPTS}
 	cp -p --remove-destination comparePublic.csh       ${SCRIPTS}
 	cp -p --remove-destination compareTableLists.csh   ${SCRIPTS}
 	cp -p --remove-destination compareTableToFile.csh  ${SCRIPTS}
 	cp -p --remove-destination compareTrackDbAll.csh   ${SCRIPTS}
 	cp -p --remove-destination compareTrackDbFast.csh  ${SCRIPTS}
 	cp -p --remove-destination compareTrackDbs.csh     ${SCRIPTS}
 	cp -p --remove-destination compareWholeColumn.csh  ${SCRIPTS}
 	cp -p --remove-destination compareWholeTable.csh   ${SCRIPTS}
 	cp -p --remove-destination copyExtSeqRows.csh      ${SCRIPTS}
 	cp -p --remove-destination copyHgcentral           ${SCRIPTS}
 	cp -p --remove-destination countPerChrom.csh       ${SCRIPTS}
 	cp -p --remove-destination countRows.csh           ${SCRIPTS}
 	cp -p --remove-destination cronLinks.csh           ${SCRIPTS}
 	cp -p --remove-destination databaseAday.csh        ${SCRIPTS}
 	cp -p --remove-destination dbUpdateTimes.csh       ${SCRIPTS}
 	cp -p --remove-destination doGenbankTests          ${SCRIPTS}
 	cp -p --remove-destination dropUserTables.csh      ${SCRIPTS}
 	cp -p --remove-destination dumpEmpty.csh           ${SCRIPTS}
 	cp -p --remove-destination findDbPartners.csh      ${SCRIPTS}
 	cp -p --remove-destination findBigFiles.csh        ${SCRIPTS}
 	cp -p --remove-destination findBlatServer.csh      ${SCRIPTS}
 	cp -p --remove-destination findBrokenLinks.csh     ${SCRIPTS}
 	cp -p --remove-destination findColumn.csh          ${SCRIPTS}
 	cp -p --remove-destination findKgTableSet.csh      ${SCRIPTS}
 	cp -p --remove-destination findLevel               ${SCRIPTS}
 	cp -p --remove-destination findMtNets.csh          ${SCRIPTS}
 	cp -p --remove-destination findNewTables.csh       ${SCRIPTS}
 	cp -p --remove-destination findOrg.csh             ${SCRIPTS}
 	cp -p --remove-destination findPushQLocks.csh      ${SCRIPTS}
 	cp -p --remove-destination gc-stats.pl             ${SCRIPTS}
 	cp -p --remove-destination genbankRun.csh          ${SCRIPTS}
 	cp -p --remove-destination generic_range_check.csh ${SCRIPTS} 
 	cp -p --remove-destination getAssemblies.csh       ${SCRIPTS}
 	cp -p --remove-destination getChainLines.csh       ${SCRIPTS}
 	cp -p --remove-destination getChromFieldName.csh   ${SCRIPTS}
 	cp -p --remove-destination getChromlist.csh        ${SCRIPTS}
 	cp -p --remove-destination getConservation.csh     ${SCRIPTS}
 	cp -p --remove-destination getDbSize.csh           ${SCRIPTS}
 	cp -p --remove-destination getField.csh            ${SCRIPTS}
 	cp -p --remove-destination getJoinerKeyErrors.pl   ${SCRIPTS}
 	cp -p --remove-destination getLastMonth.csh        ${SCRIPTS}
 	cp -p --remove-destination getLiftOver.csh         ${SCRIPTS}
 	cp -p --remove-destination getMatrixLines.csh      ${SCRIPTS}
 	cp -p --remove-destination getMonthLastYear.csh    ${SCRIPTS}
 	cp -p --remove-destination getOrderKey.csh         ${SCRIPTS}
 	cp -p --remove-destination getRRdatabases.csh      ${SCRIPTS}
 	cp -p --remove-destination getRRdumpfile.csh       ${SCRIPTS}
 	cp -p --remove-destination getRRtableStatus.csh    ${SCRIPTS}
 	cp -p --remove-destination getRRtables.csh         ${SCRIPTS}
 	cp -p --remove-destination getTableSize.csh        ${SCRIPTS}
 	cp -p --remove-destination getTableStatus.csh      ${SCRIPTS}
 	cp -p --remove-destination getTrackName.csh        ${SCRIPTS}
 	cp -p --remove-destination getSplit.csh            ${SCRIPTS}
 	cp -p --remove-destination getVersion.csh          ${SCRIPTS}
 	cp -p --remove-destination getYield.csh            ${SCRIPTS}
 	cp -p --remove-destination graph.csh               ${SCRIPTS}
 	cp -p --remove-destination igtc.csh                ${SCRIPTS}
 	cp -p --remove-destination idHitter.csh            ${SCRIPTS}
 	cp -p --remove-destination joinerBatchKeys.csh     ${SCRIPTS}
 	cp -p --remove-destination joinerBatchTimes.csh    ${SCRIPTS}
 	cp -p --remove-destination kgTables                ${SCRIPTS}
 	cp -p --remove-destination gsTables                ${SCRIPTS}
 	cp -p --remove-destination pbTables                ${SCRIPTS}
 	cp -p --remove-destination knownGene.csh           ${SCRIPTS}
 	cp -p --remove-destination linkCheckExclude        ${SCRIPTS}
 	cp -p --remove-destination makeCytoBandIdeo.csh    ${SCRIPTS}
 	cp -p --remove-destination makeFilledBlockBed.csh  ${SCRIPTS}
 	cp -p --remove-destination makeTouchCommands.csh   ${SCRIPTS}
 	cp -p --remove-destination makeUniProtFile.csh     ${SCRIPTS}
 	cp -p --remove-destination net.csh                 ${SCRIPTS}
 	cp -p --remove-destination proteins.csh            ${SCRIPTS}
 	cp -p --remove-destination printMan.csh            ${SCRIPTS}
+	cp -p --remove-destination qaAutoTrack.sh          ${SCRIPTS}
 	cp -p --remove-destination qaConfig.csh            ${SCRIPTS}
 	cp -p --remove-destination qaConfig.bash           ${SCRIPTS}
 	cp -p --remove-destination qaGbTracks              ${SCRIPTS}
 	cp -p --remove-destination qaEncodeTracks.csh      ${SCRIPTS}
 	cp -p --remove-destination qaEnsGenes.csh          ${SCRIPTS}
 	cp -p --remove-destination qaThis.csh              ${SCRIPTS}
 	cp -p --remove-destination realTime.csh            ${SCRIPTS}
 	cp -p --remove-destination removeAlphas            ${SCRIPTS}
 	cp -p --remove-destination retirePushQ.csh         ${SCRIPTS}
 	cp -p --remove-destination runBits.csh             ${SCRIPTS}
 	cp -p --remove-destination runCheckHgFindSpec      ${SCRIPTS}
 	cp -p --remove-destination runJoiner.csh           ${SCRIPTS}
 	cp -p --remove-destination sessionStats.csh        ${SCRIPTS}
 	cp -p --remove-destination showLastGit.csh         ${SCRIPTS}
 	cp -p --remove-destination showProcesslist.csh     ${SCRIPTS}
 	cp -p --remove-destination staticpaths             ${SCRIPTS}
 	cp -p --remove-destination syncAday.csh            ${SCRIPTS}
 	cp -p --remove-destination trackDbGlobal.csh       ${SCRIPTS}
 	cp -p --remove-destination updateTimes.csh         ${SCRIPTS}
 	cp -p --remove-destination updateTimesDb.sh        ${SCRIPTS}
 	cp -p --remove-destination whoMadeIt.csh           ${SCRIPTS}
 	@echo Reminder: was your sandbox up to date?
 
 clean::
 	@echo nothing to clean in src/utils/qa/