0ac694cd00be11bb7ccf3a678e3d8af7fecce04b
galt
  Wed Aug 12 12:16:05 2015 -0700
Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option.  Jing says it is OK to nuke this old junk. Of course it will live in history as it should.

diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 934e527..183e284 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -1,310 +1,308 @@
 #!/bin/bash
 #
 # exit on any error:
 set -beEu -o pipefail
 
 # switching to beta for version 286
 export branch="beta"
 
 # to use the top of the source tree, uncomment this branch=HEAD statment
 # and comment out the one above.  This is sometimes useful when there
 # are new fixes in the source tree in between beta releases.
 # Note, the top of the source tree could be broken at any time, it is on
 # a 10-minute update cycle with live work taking place.
 
 # export branch="HEAD"
 
 # script to fetch extra source to use with the kent build,
 # and then selectively parts of the kent source tree, enough to
 # build just the user utilities
 
 # the combined samtabix source for the SAM/BAM/TABIX functions:
 rm -fr samtabix
 echo "fetch samtabix" 1>&2
 git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix \
   > /dev/null 2>&1
 
 # These selective git archive commands only work up to a certain size
 # of fetched source (number of arguments), hence the multiple set of
 # individual fetches to get all the parts
 
 rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip part5Src.zip
 export partNumber=1
 export ofN="of 5"
 
 # this util changed from being in a directory to being a script
 # the extract can't overwrite the directory with a file
 rm -fr kent/src/utils/uniprotLift
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/checkUmask.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/index \
 src/makefile \
 src/meta \
 src/parasol \
 src/primeMate \
 src/product \
 src/protDust \
 src/weblet \
 src/inc \
 src/utils \
 src/jkOwnLib \
 src/lib \
 src/hg/affyTransciptome \
 src/hg/agpAllToFaFile \
 src/hg/agpCloneCheck \
 src/hg/agpCloneList \
 src/hg/agpToFa \
 src/hg/agpToGl \
 src/hg/altSplice \
 src/hg/autoDtd \
 src/hg/autoSql \
 src/hg/autoXml \
 src/hg/bedIntersect \
 src/hg/bedItemOverlapCount \
 src/hg/bedOrBlocks \
 src/hg/bedSort \
 src/hg/bedSplitOnChrom \
 src/hg/bedToGenePred \
 src/hg/blastToPsl \
 src/hg/borfBig \
 src/hg/checkCoverageGaps \
 src/hg/checkHgFindSpec \
 src/hg/checkTableCoords \
 src/hg/ctgFaToFa \
 src/hg/ctgToChromFa \
 src/hg/dbTrash \
 src/hg/embossToPsl \
 src/hg/estOrient \
 src/hg/encode/validateFiles \
 src/hg/fakeFinContigs \
 src/hg/fakeOut \
 src/hg/featureBits \
 src/hg/ffaToFa \
 src/hg/fishClones \
 src/hg/fqToQa \
 src/hg/fqToQac \
 src/hg/fragPart \
 src/hg/gbGetEntries \
 src/hg/gbOneAcc > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/gbToFaRa \
 src/hg/geneBounds \
 src/hg/genePredHisto \
 src/hg/genePredSingleCover \
 src/hg/genePredToBed \
 src/hg/genePredToFakePsl \
 src/hg/genePredToGtf \
 src/hg/genePredToMafFrames \
 src/hg/getFeatDna \
 src/hg/getRna \
 src/hg/getRnaPred \
 src/hg/gpStats \
 src/hg/gpToGtf \
 src/hg/gpcrParser \
 src/hg/gsBig \
 src/hg/hgChroms \
 src/hg/hgGetAnn \
 src/hg/hgKnownGeneList \
 src/hg/hgSelect \
 src/hg/hgSpeciesRna \
 src/hg/hgTablesTest \
 src/hg/hgsql \
-src/hg/hgsqlLocal \
 src/hg/hgsqlSwapTables \
 src/hg/hgsqlTableDate \
 src/hg/hgsqladmin \
 src/hg/hgsqldump \
-src/hg/hgsqldumpLocal \
 src/hg/hgsqlimport \
 src/hg/inc \
 src/hg/intronEnds \
 src/hg/lib \
 src/hg/lfsOverlap \
 src/hg/liftAcross \
 src/hg/liftAgp \
 src/hg/liftFrags \
 src/hg/liftUp \
 src/hg/liftOver \
 src/hg/makefile \
 src/hg/makeDb/hgLoadWiggle \
 src/hg/makeDb/hgGcPercent \
 src/hg/utils \
 src/hg/maskOutFa \
 src/hg/mdToNcbiLift \
 src/hg/mrnaToGene \
 src/hg/orthoMap \
 src/hg/patCount \
 src/hg/perf \
 src/hg/pslCat \
 src/hg/pslCheck \
 src/hg/pslCoverage \
 src/hg/pslCDnaFilter \
 src/hg/pslPretty \
 src/hg/pslReps \
 src/hg/pslSort \
 src/hg/pslDropOverlap > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/pslFilter \
 src/hg/pslFilterPrimers \
 src/hg/pslGlue \
 src/hg/pslHisto \
 src/hg/pslHitPercent \
 src/hg/pslIntronsOnly \
 src/hg/pslPairs \
 src/hg/pslPartition \
 src/hg/pslQuickFilter \
 src/hg/pslRecalcMatch \
 src/hg/pslSelect \
 src/hg/pslSimp \
 src/hg/pslSortAcc \
 src/hg/pslSplitOnTarget \
 src/hg/pslStats \
 src/hg/pslSwap \
 src/hg/pslToBed \
 src/hg/pslUnpile \
 src/hg/pslxToFa \
 src/hg/qa \
 src/hg/qaToQac \
 src/hg/qacAgpLift \
 src/hg/qacToQa \
 src/hg/qacToWig \
 src/hg/recycleDb \
 src/hg/relPairs \
 src/hg/reviewSanity \
 src/hg/rnaStructure \
 src/hg/scanRa \
 src/hg/semiNorm \
 src/hg/sim4big \
 src/hg/snp \
 src/hg/snpException \
 src/hg/spideyToPsl \
 src/hg/encode3 \
 src/hg/splitFa \
 src/hg/splitFaIntoContigs \
 src/hg/sqlEnvTest.sh \
 src/hg/sqlToXml \
 src/hg/test \
 src/hg/trfBig \
 src/hg/txCds \
 src/hg/txGene \
 src/hg/txGraph \
 src/hg/uniqSize \
 src/hg/updateStsInfo \
 src/hg/xmlCat \
 src/hg/xmlToSql \
 src/hg/hgTables \
 src/hg/near \
 src/hg/pslDiff \
 src/hg/sage \
 src/hg/gigAssembler/checkAgpAndFa \
 src/hg/genePredCheck > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/makeDb/makefile \
 src/hg/makeDb/hgAar \
 src/hg/makeDb/hgAddLiftOverChain \
 src/hg/makeDb/hgBbiDbLink \
 src/hg/makeDb/hgClonePos \
 src/hg/makeDb/hgCountAlign \
 src/hg/makeDb/hgCtgPos \
 src/hg/makeDb/hgDeleteChrom \
 src/hg/makeDb/hgExperiment \
 src/hg/makeDb/hgExtFileCheck \
 src/hg/makeDb/hgFakeAgp \
 src/hg/makeDb/hgFindSpec \
 src/hg/makeDb/hgGeneBands \
 src/hg/makeDb/hgGenericMicroarray \
 src/hg/makeDb/hgPar \
 src/hg/makeDb/hgGoldGapGl \
 src/hg/makeDb/hgKgGetText \
 src/hg/makeDb/hgKgMrna \
 src/hg/makeDb/hgKnownMore \
 src/hg/makeDb/hgKnownMore.oo21 \
 src/hg/makeDb/hgLoadBed \
 src/hg/makeDb/hgLoadBlastTab \
 src/hg/makeDb/hgLoadChain \
 src/hg/makeDb/hgLoadChromGraph \
 src/hg/makeDb/hgLoadGenePred \
 src/hg/makeDb/hgLoadItemAttr \
 src/hg/makeDb/hgLoadMaf \
 src/hg/makeDb/hgLoadMafFrames \
 src/hg/makeDb/hgLoadNet \
 src/hg/makeDb/hgLoadOut \
 src/hg/makeDb/hgLoadOutJoined \
 src/hg/makeDb/hgLoadPsl \
 src/hg/makeDb/hgLoadSeq \
 src/hg/makeDb/hgLoadSample \
 src/hg/makeDb/hgLoadSqlTab \
 src/hg/makeDb/hgMapMicroarray \
 src/hg/makeDb/hgMedianMicroarray \
 src/hg/makeDb/hgNibSeq \
 src/hg/makeDb/hgPepPred \
 src/hg/makeDb/hgRatioMicroarray \
 src/hg/makeDb/hgDropSplitTable \
 src/hg/makeDb/hgRenameSplitTable \
 src/hg/makeDb/hgSanger20 \
 src/hg/makeDb/hgSanger22 \
 src/hg/makeDb/hgStanfordMicroarray \
 src/hg/makeDb/hgStsAlias \
 src/hg/makeDb/hgStsMarkers \
 src/hg/makeDb/hgTomRough \
 src/hg/makeDb/hgTpf \
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/parasol \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
 src/hg/visiGene/hgVisiGene > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip