edb6fc7755da47df33f2dce4af4fd0017385b7fc
hiram
  Thu Jun 11 12:55:46 2026 -0700
hacking in the submodules for the htslib no redmine

diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 3b7dd3f802f..4856b4db4e1 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -16,31 +16,33 @@
 
 # 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
+cd src/submodules
+./submoduleSetup
+cd ../..
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/checkUmask.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/isPcr \
 src/index \
 src/makefile \
@@ -265,48 +267,51 @@
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > ../part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --prefix=kent/ ${branch} \
 src/parasol \
 src/tabFile \
-src/submodules/htslib \
 src/optimalLeaf \
+src/submodules \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/makeDb/dbDbToHubTxt \
 src/hg/makeDb/trackDbToTxt \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
 src/hg/visiGene/hgVisiGene > ../part${partNumber}Src.zip
 
 cd ..
 du -hsc kent-temp
-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
+
+rsync -a kent-temp/src/submodules/ kent/src/submodules/
+
+rm -rf kent-temp