e617d8fcfd4f783bfe7e3b569c620532ab43858d
markd
  Wed Jun 10 01:32:09 2026 -0700
fix #37741 Source zip (jksrc.zip) build broken: htslib submodule not included by git archive

diff --git src/utils/qa/weeklybld/coBranch.csh src/utils/qa/weeklybld/coBranch.csh
index 6edf639c5d6..e06f30ada7e 100755
--- src/utils/qa/weeklybld/coBranch.csh
+++ src/utils/qa/weeklybld/coBranch.csh
@@ -1,45 +1,52 @@
 #!/bin/tcsh
 
 cd $WEEKLYBLD
 
 echo "BRANCHNN=$BRANCHNN"
 if ( "$BRANCHNN" == "" ) then
  echo "BRANCHNN undefined."
  exit 1
 endif
 
 echo
 echo "now unpacking new branch $BRANCHNN on `uname -n` [${0}: `date`]"
 
 #unpack the new branch on BUILDDIR for beta
 # for later: is this faster to co on kkstore or not?
 cd $BUILDDIR
 set branch = "v"$BRANCHNN"_branch" 
 if ( -d $branch ) then
  echo "removing old branch dir. [${0}: `date`]"
  rm -fr $branch 
 endif
 mkdir -p $branch
 cd $branch
 echo "Checking out branch $BRANCHNN. [${0}: `date`]"
 git clone -q $GITSHAREDREPO kent
 chmod g+w kent
 cd kent
 git checkout --track=direct -b $branch origin/$branch
 set err = $status
 if ( $err ) then
  echo "error running git clone and checkout of kent in $BUILDDIR/$branch : $err [${0}: `date`]"
  exit 1
 endif
+# check out submodules (e.g. src/submodules/htslib) for the branch
+git submodule update --init --recursive
+set err = $status
+if ( $err ) then
+ echo "error updating submodules of kent in $BUILDDIR/$branch : $err [${0}: `date`]"
+ exit 1
+endif
 cd ..
 
 
 # configure settings like SSL and BAM in common.mk
 echo "Configuring settings on branch $BRANCHNN in $BUILDDIR/$branch [${0}: `date`]" 
 $WEEKLYBLD/configureSandbox.csh . $WEEKLYBLD/defaultBuildSettings.mk
 
 echo "Done checking out branch $BRANCHNN in $BUILDDIR/$branch [${0}: `date`]" 
 echo "Now you should go and do build on beta! [${0}: `date`]"
 
 exit 0