9431ca8ba35a97885ab78a6a4fa997e05d68fd12
hiram
  Thu Dec 11 15:26:16 2025 -0800
can not use the genome-test.soe.ucsc.edu/kent.git server outside UCSC environment refs #36817

diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 77de3c47855..86773ead3ab 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -7,43 +7,42 @@
 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"
 
 # 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
+rm -fr kent-temp
 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
-# v385 this util changed from a script by this name to a directory
-# and the script changed to a .py name
-rm -fr kent/src/utils/bedJoinTabOffset
+git clone --depth=1 --branch=${branch} \
+    https://github.com/ucscGenomeBrowser/kent.git kent-temp
+cd kent-temp
+
+git checkout ${branch}
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
-git archive --format=zip -9 --remote=git://genome-test.soe.ucsc.edu/kent.git \
---prefix=kent/ ${branch} \
+git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/checkUmask.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/isPcr \
 src/index \
 src/makefile \
 src/meta \
 src/parasol \
 src/primeMate \
@@ -78,39 +77,36 @@
 src/hg/checkTableCoords \
 src/hg/ctgFaToFa \
 src/hg/ctgToChromFa \
 src/hg/dbTrash \
 src/hg/embossToPsl \
 src/hg/estOrient \
 src/hg/fakeFinContigs \
 src/hg/fakeOut \
 src/hg/featureBits \
 src/hg/ffaToFa \
 src/hg/fishClones \
 src/hg/fqToQa \
 src/hg/fqToQac \
 src/hg/fragPart \
 src/hg/gbGetEntries \
-src/hg/gbOneAcc > part${partNumber}Src.zip
-
-unzip -o -q part${partNumber}Src.zip
+src/hg/gbOneAcc > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
-git archive --format=zip -9 --remote=git://genome-test.soe.ucsc.edu/kent.git \
---prefix=kent/ ${branch} \
+git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/hg/gbToFaRa \
 src/hg/geneBounds \
 src/hg/genePredHisto \
 src/hg/genePredSingleCover \
 src/hg/genePredToBed \
 src/hg/genePredToFakePsl \
 src/hg/genePredToGtf \
 src/hg/genePredToMafFrames \
 src/hg/getFeatDna \
 src/hg/getRna \
 src/hg/getRnaPred \
 src/hg/gpStats \
 src/hg/gpToGtf \
 src/hg/gpcrParser \
 src/hg/gsBig \
@@ -141,39 +137,36 @@
 src/hg/utils \
 src/hg/maskOutFa \
 src/hg/mdToNcbiLift \
 src/hg/mrnaToGene \
 src/hg/orthoMap \
 src/hg/patCount \
 src/hg/perf \
 src/hg/pslCat \
 src/hg/pslCheck \
 src/hg/pslCoverage \
 src/hg/pslCDnaFilter \
 src/hg/pslPretty \
 src/hg/pslReps \
 src/hg/pslSort \
 src/hg/pslSomeRecords \
-src/hg/pslDropOverlap > part${partNumber}Src.zip
-
-unzip -o -q part${partNumber}Src.zip
+src/hg/pslDropOverlap > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
-git archive --format=zip -9 --remote=git://genome-test.soe.ucsc.edu/kent.git \
---prefix=kent/ ${branch} \
+git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/hg/pslFilter \
 src/hg/pslFilterPrimers \
 src/hg/pslGlue \
 src/hg/pslHisto \
 src/hg/pslHitPercent \
 src/hg/pslIntronsOnly \
 src/hg/pslPairs \
 src/hg/pslPartition \
 src/hg/pslQuickFilter \
 src/hg/pslRecalcMatch \
 src/hg/pslSelect \
 src/hg/pslSimp \
 src/hg/pslSortAcc \
 src/hg/pslSplitOnTarget \
 src/hg/pslStats \
@@ -201,39 +194,36 @@
 src/hg/sqlToXml \
 src/hg/test \
 src/hg/trfBig \
 src/hg/txCds \
 src/hg/txGene \
 src/hg/txGraph \
 src/hg/uniqSize \
 src/hg/updateStsInfo \
 src/hg/xmlCat \
 src/hg/xmlToSql \
 src/hg/hgTables \
 src/hg/near \
 src/hg/pslDiff \
 src/hg/sage \
 src/hg/gigAssembler/checkAgpAndFa \
-src/hg/genePredCheck > part${partNumber}Src.zip
-
-unzip -o -q part${partNumber}Src.zip
+src/hg/genePredCheck > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
-git archive --format=zip -9 --remote=git://genome-test.soe.ucsc.edu/kent.git \
---prefix=kent/ ${branch} \
+git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/hg/makeDb/makefile \
 src/hg/makeDb/hgAar \
 src/hg/makeDb/hgAddLiftOverChain \
 src/hg/makeDb/hgBbiDbLink \
 src/hg/makeDb/hgClonePos \
 src/hg/makeDb/hgCountAlign \
 src/hg/makeDb/hgCtgPos \
 src/hg/makeDb/hgDeleteChrom \
 src/hg/makeDb/hgExperiment \
 src/hg/makeDb/hgExtFileCheck \
 src/hg/makeDb/hgFakeAgp \
 src/hg/makeDb/hgFindSpec \
 src/hg/makeDb/hgGeneBands \
 src/hg/makeDb/hgGenericMicroarray \
 src/hg/makeDb/hgPar \
@@ -266,41 +256,55 @@
 src/hg/makeDb/hgRenameSplitTable \
 src/hg/makeDb/hgSanger20 \
 src/hg/makeDb/hgSanger22 \
 src/hg/makeDb/hgStanfordMicroarray \
 src/hg/makeDb/hgStsAlias \
 src/hg/makeDb/hgStsMarkers \
 src/hg/makeDb/hgTomRough \
 src/hg/makeDb/hgTpf \
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
-src/hg/makeDb/tfbsConsSort > part${partNumber}Src.zip
-
-unzip -o -q part${partNumber}Src.zip
+src/hg/makeDb/tfbsConsSort > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
-git archive --format=zip -9 --remote=git://genome-test.soe.ucsc.edu/kent.git \
---prefix=kent/ ${branch} \
+git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/parasol \
 src/tabFile \
 src/htslib \
 src/optimalLeaf \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/makeDb/dbDbToHubTxt \
 src/hg/makeDb/trackDbToTxt \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
-src/hg/visiGene/hgVisiGene > part${partNumber}Src.zip
+src/hg/visiGene/hgVisiGene > ../part${partNumber}Src.zip
 
+cd ..
+rm -rf kent-temp
+
+partNumber=1
+echo "unzip source part ${partNumber} ${ofN}" 1>&2
+unzip -o -q part${partNumber}Src.zip
+((partNumber++))
+echo "unzip source part ${partNumber} ${ofN}" 1>&2
+unzip -o -q part${partNumber}Src.zip
+((partNumber++))
+echo "unzip source part ${partNumber} ${ofN}" 1>&2
+unzip -o -q part${partNumber}Src.zip
+((partNumber++))
+echo "unzip source part ${partNumber} ${ofN}" 1>&2
+unzip -o -q part${partNumber}Src.zip
+((partNumber++))
+echo "unzip source part ${partNumber} ${ofN}" 1>&2
 unzip -o -q part${partNumber}Src.zip