1fd0ab8b59002435f0da06a8c5f1525db09024dc
markd
  Thu Apr 30 20:52:15 2026 -0700
inital conversion of fetchKentSource, can not test until on github

diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 98d3d9f635a..3b7dd3f802f 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -16,30 +16,31 @@
 
 # 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"
 
 git clone --depth=1 --branch=${branch} \
     https://github.com/ucscGenomeBrowser/kent.git kent-temp
 cd kent-temp
 
 git checkout ${branch}
+git -c protocol.file.allow=always submodule update --init --recursive
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/checkUmask.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/isPcr \
 src/index \
 src/makefile \
@@ -264,31 +265,31 @@
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/parasol \
 src/tabFile \
-src/htslib \
+src/submodules/htslib \
 src/optimalLeaf \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/makeDb/dbDbToHubTxt \
 src/hg/makeDb/trackDbToTxt \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
 src/hg/visiGene/hgVisiGene > ../part${partNumber}Src.zip
 
 cd ..
 du -hsc kent-temp