6c6176de07f6282d2f6fde65e8210a4a8eeef09c
hiram
  Thu May 23 10:30:35 2013 -0700
adjusting README instructions and expanding the fetch operation refs #9104
diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 197ab41..3710384 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -1,48 +1,151 @@
 #!/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
+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"
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ HEAD \
 src/machTest.sh \
 src/ameme \
 src/aladdin \
 src/blat \
-src/cdnaAli \
 src/dnaDust \
 src/fuse \
-src/getgene \
 src/gfClient \
 src/gfServer \
-src/idbQuery \
 src/index \
 src/makefile \
 src/meta \
 src/primeMate \
 src/product \
 src/protDust \
-src/reformat \
-src/scanIntrons \
-src/tracks \
 src/weblet \
-src/wormAli \
-src/xenoAli \
 src/inc \
 src/utils \
 src/jkOwnLib \
-src/lib > part${partNumber}.zip
+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