909fa0bac52797915a8ac240f595d0ca0bf304f1
hiram
  Thu May 23 11:10:43 2013 -0700
adding auto detection of mysql lib installs and more userApps source fetch refs #9104
diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 3710384..624318b 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -1,151 +1,292 @@
 #!/bin/bash
 #
 # exit on any error:
 set -beEu -o pipefail
 
 # 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, hence the multiple set of individual fetches to
 # get all the parts
 
 rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip
 export partNumber=1
-export ofN="of 6"
+export ofN="of 5"
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ HEAD \
 src/machTest.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/index \
 src/makefile \
 src/meta \
 src/primeMate \
 src/product \
 src/protDust \
 src/weblet \
 src/inc \
 src/utils \
 src/jkOwnLib \
 src/lib \
 src/hg/affyTransciptome \
 src/hg/agpAllToFaFile \
 src/hg/agpCloneCheck \
 src/hg/agpCloneList \
 src/hg/agpToFa \
 src/hg/agpToGl \
 src/hg/altSplice \
 src/hg/autoDtd \
 src/hg/autoSql \
 src/hg/autoXml \
 src/hg/bedIntersect \
 src/hg/bedItemOverlapCount \
 src/hg/bedOrBlocks \
 src/hg/bedSort \
 src/hg/bedSplitOnChrom \
 src/hg/bedToGenePred \
 src/hg/blastToPsl \
 src/hg/borfBig \
 src/hg/checkCoverageGaps \
 src/hg/checkHgFindSpec \
 src/hg/checkTableCoords \
 src/hg/ctgFaToFa \
 src/hg/ctgToChromFa \
 src/hg/dbTrash \
 src/hg/embossToPsl \
 src/hg/estOrient \
 src/hg/encode/validateFiles \
 src/hg/fakeFinContigs \
 src/hg/fakeOut \
 src/hg/featureBits \
 src/hg/ffaToFa \
 src/hg/fishClones \
 src/hg/fqToQa \
 src/hg/fqToQac \
 src/hg/fragPart \
 src/hg/gbGetEntries \
 src/hg/gbOneAcc \
 src/hg/gbToFaRa > part${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/ HEAD \
 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} ${ofN}" 1>&2
+
+git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
+--prefix=kent/ HEAD \
+src/hg/pslFilter \
+src/hg/pslFilterPrimers \
+src/hg/pslGlue \
+src/hg/pslHisto \
+src/hg/pslHitPercent \
+src/hg/pslIntronsOnly \
+src/hg/pslPairs \
+src/hg/pslPartition \
+src/hg/pslQuickFilter \
+src/hg/pslRecalcMatch \
+src/hg/pslSelect \
+src/hg/pslSimp \
+src/hg/pslSortAcc \
+src/hg/pslSplitOnTarget \
+src/hg/pslStats \
+src/hg/pslSwap \
+src/hg/pslToBed \
+src/hg/pslUnpile \
+src/hg/pslxToFa \
+src/hg/qa \
+src/hg/qaToQac \
+src/hg/qacAgpLift \
+src/hg/qacToQa \
+src/hg/qacToWig \
+src/hg/ratStuff/mafsInRegion \
+src/hg/ratStuff/mafSpeciesSubset \
+src/hg/recycleDb \
+src/hg/relPairs \
+src/hg/reviewSanity \
+src/hg/rnaStructure \
+src/hg/scanRa \
+src/hg/semiNorm \
+src/hg/sim4big \
+src/hg/snp \
+src/hg/snpException \
+src/hg/spideyToPsl \
+src/hg/encode3 \
+src/hg/splitFa \
+src/hg/splitFaIntoContigs \
+src/hg/sqlEnvTest.sh \
+src/hg/sqlToXml \
+src/hg/test \
+src/hg/trfBig \
+src/hg/txCds \
+src/hg/txGene \
+src/hg/txGraph \
+src/hg/uniqSize \
+src/hg/updateStsInfo \
+src/hg/xmlCat \
+src/hg/xmlToSql \
+src/hg/hgTables \
+src/hg/near \
+src/hg/pslDiff \
+src/hg/sage \
+src/hg/gigAssembler/checkAgpAndFa \
+src/hg/genePredCheck > part${partNumber}Src.zip
+
+unzip -o -q part${partNumber}Src.zip
+
+((partNumber++))
+echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
+
+git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
+--prefix=kent/ HEAD \
+src/hg/makeDb/makefile \
+src/hg/makeDb/hgAar \
+src/hg/makeDb/hgAddLiftOverChain \
+src/hg/makeDb/hgBbiDbLink \
+src/hg/makeDb/hgClonePos \
+src/hg/makeDb/hgCountAlign \
+src/hg/makeDb/hgCtgPos \
+src/hg/makeDb/hgDeleteChrom \
+src/hg/makeDb/hgExperiment \
+src/hg/makeDb/hgExtFileCheck \
+src/hg/makeDb/hgFakeAgp \
+src/hg/makeDb/hgFindSpec \
+src/hg/makeDb/hgGeneBands \
+src/hg/makeDb/hgGenericMicroarray \
+src/hg/makeDb/hgPar \
+src/hg/makeDb/hgGoldGapGl \
+src/hg/makeDb/hgKgGetText \
+src/hg/makeDb/hgKgMrna \
+src/hg/makeDb/hgKnownMore \
+src/hg/makeDb/hgKnownMore.oo21 \
+src/hg/makeDb/hgLoadBed \
+src/hg/makeDb/hgLoadBlastTab \
+src/hg/makeDb/hgLoadChain \
+src/hg/makeDb/hgLoadChromGraph \
+src/hg/makeDb/hgLoadGenePred \
+src/hg/makeDb/hgLoadItemAttr \
+src/hg/makeDb/hgLoadMaf \
+src/hg/makeDb/hgLoadMafFrames \
+src/hg/makeDb/hgLoadNet \
+src/hg/makeDb/hgLoadOut \
+src/hg/makeDb/hgLoadPsl \
+src/hg/makeDb/hgLoadSeq \
+src/hg/makeDb/hgLoadSample \
+src/hg/makeDb/hgLoadSqlTab \
+src/hg/makeDb/hgMapMicroarray \
+src/hg/makeDb/hgMedianMicroarray \
+src/hg/makeDb/hgNibSeq \
+src/hg/makeDb/hgPepPred \
+src/hg/makeDb/hgRatioMicroarray \
+src/hg/makeDb/hgDropSplitTable \
+src/hg/makeDb/hgRenameSplitTable \
+src/hg/makeDb/hgSanger20 \
+src/hg/makeDb/hgSanger22 \
+src/hg/makeDb/hgStanfordMicroarray \
+src/hg/makeDb/hgStsAlias \
+src/hg/makeDb/hgStsMarkers \
+src/hg/makeDb/hgTomRough \
+src/hg/makeDb/hgTpf \
+src/hg/makeDb/hgTraceInfo \
+src/hg/makeDb/hgTrackDb \
+src/hg/makeDb/hgWaba \
+src/hg/makeDb/ldHgGene \
+src/hg/makeDb/hgMrnaRefseq \
+src/hg/makeDb/schema \
+src/hg/makeDb/tfbsConsLoc \
+src/hg/makeDb/tfbsConsSort > part${partNumber}Src.zip
+
+unzip -o -q part${partNumber}Src.zip
+
+((partNumber++))
+echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
+
+git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
+--prefix=kent/ HEAD \
+src/hg/makeDb/outside \
+src/hg/makeDb/trackDbRaFormat \
+src/hg/makeDb/trackDbPatch \
+src/hg/mouseStuff \
+src/hg/ratStuff \
+src/hg/nci60 \
+src/hg/visiGene/knownToVisiGene \
+src/hg/visiGene/hgVisiGene > part${partNumber}Src.zip
+
+unzip -o -q part${partNumber}Src.zip