80a15125d2da7746fb4c77e03df4b7f5a8254753
hiram
  Wed Jun 26 11:25:15 2013 -0700
ready for v286 with the beta branch fetch instead of HEAD refs #9149
diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index b3636e0..81ea3bf 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -1,41 +1,46 @@
 #!/bin/bash
 #
 # exit on any error:
 set -beEu -o pipefail
 
+# for version 286 we will use beta branch instead of HEAD
+# export branch="beta"
+
+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"
 
 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 \
+--prefix=kent/ ${branch} \
 src/machTest.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/index \
 src/makefile \
 src/meta \
 src/parasol \
 src/primeMate \
 src/product \
 src/protDust \
@@ -76,31 +81,31 @@
 src/hg/featureBits \
 src/hg/ffaToFa \
 src/hg/fishClones \
 src/hg/fqToQa \
 src/hg/fqToQac \
 src/hg/fragPart \
 src/hg/gbGetEntries \
 src/hg/gbOneAcc > part${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/ HEAD \
+--prefix=kent/ ${branch} \
 src/hg/gbToFaRa \
 src/hg/geneBounds \
 src/hg/genePredHisto \
 src/hg/genePredSingleCover \
 src/hg/genePredToBed \
 src/hg/genePredToFakePsl \
 src/hg/genePredToGtf \
 src/hg/genePredToMafFrames \
 src/hg/getFeatDna \
 src/hg/getRna \
 src/hg/getRnaPred \
 src/hg/gpStats \
 src/hg/gpToGtf \
 src/hg/gpcrParser \
 src/hg/gsBig \
@@ -140,31 +145,31 @@
 src/hg/pslCat \
 src/hg/pslCheck \
 src/hg/pslCoverage \
 src/hg/pslCDnaFilter \
 src/hg/pslPretty \
 src/hg/pslReps \
 src/hg/pslSort \
 src/hg/pslDropOverlap > part${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 \
+--prefix=kent/ ${branch} \
 src/hg/pslFilter \
 src/hg/pslFilterPrimers \
 src/hg/pslGlue \
 src/hg/pslHisto \
 src/hg/pslHitPercent \
 src/hg/pslIntronsOnly \
 src/hg/pslPairs \
 src/hg/pslPartition \
 src/hg/pslQuickFilter \
 src/hg/pslRecalcMatch \
 src/hg/pslSelect \
 src/hg/pslSimp \
 src/hg/pslSortAcc \
 src/hg/pslSplitOnTarget \
 src/hg/pslStats \
@@ -204,31 +209,31 @@
 src/hg/xmlCat \
 src/hg/xmlToSql \
 src/hg/hgTables \
 src/hg/near \
 src/hg/pslDiff \
 src/hg/sage \
 src/hg/gigAssembler/checkAgpAndFa \
 src/hg/genePredCheck > part${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 \
+--prefix=kent/ ${branch} \
 src/hg/makeDb/makefile \
 src/hg/makeDb/hgAar \
 src/hg/makeDb/hgAddLiftOverChain \
 src/hg/makeDb/hgBbiDbLink \
 src/hg/makeDb/hgClonePos \
 src/hg/makeDb/hgCountAlign \
 src/hg/makeDb/hgCtgPos \
 src/hg/makeDb/hgDeleteChrom \
 src/hg/makeDb/hgExperiment \
 src/hg/makeDb/hgExtFileCheck \
 src/hg/makeDb/hgFakeAgp \
 src/hg/makeDb/hgFindSpec \
 src/hg/makeDb/hgGeneBands \
 src/hg/makeDb/hgGenericMicroarray \
 src/hg/makeDb/hgPar \
@@ -268,28 +273,28 @@
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > part${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 \
+--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