af1467a374f0fdbaaadc073a27e8ad2465efad80
chmalee
  Tue May 18 17:01:58 2021 -0700
isPcr added to userApps

diff --git src/utils/qa/weeklybld/makeUserApps.csh src/utils/qa/weeklybld/makeUserApps.csh
index 8771edb..c14dc0d 100755
--- src/utils/qa/weeklybld/makeUserApps.csh
+++ src/utils/qa/weeklybld/makeUserApps.csh
@@ -1,73 +1,74 @@
 #!/bin/tcsh
 # ------------------------------------
 # Note - this script assumes you have your ssh key in
 # qateam@hgdownload:.ssh/authorized_keys. Without it,
 #  this script can NOT be launched from dev
 # ------------------------------------
 
 set ScriptStart=`date`
 
 echo "Cleaning out $BUILDDIR/userApps"
 rm -fr $BUILDDIR/userApps
 mkdir $BUILDDIR/userApps
 
 cd $BUILDDIR/userApps
 
 echo "Checking out kent/src branch $BRANCHNN. [${0}: `date`]"
 
 set branch = "v"$BRANCHNN"_branch"
 
 git clone -q $GITSHAREDREPO kent
 chmod g+w kent
 cd kent
 git checkout -tb $branch origin/$branch
 set err = $status
 if ( $err ) then
  echo "error running git clone and checkout of kent in $BUILDDIR/userApps : $err [${0}: `date`]" 
  exit 1
 endif 
 cd ..
 
 set BINDIR=linux.$MACHTYPE
 set DESTDIR=$BUILDDIR/userApps/  # must end in slash because of makefile weirdness
 rm -rf $DESTDIR$BINDIR
 mkdir $DESTDIR$BINDIR
 
 # configure settings like SSL and BAM in common.mk
 echo "Configuring settings on userApp sandbox $BRANCHNN $HOST [${0}: `date`]"
 $WEEKLYBLD/configureSandbox.csh . $WEEKLYBLD/downloadBuildSettings.mk
 
 cd kent/src 
 make -j 12 BINDIR=$BINDIR DESTDIR=$DESTDIR userApps > make.log
 ./utils/userApps/mkREADME.sh $DESTDIR$BINDIR FOOTER.txt
 cd ../..
 
 # copy everything if 64 bit
 if ("$HOST" == "hgwdev") then
   #clear out the old and copy in the new
   foreach f ( ${DESTDIR}${BINDIR}/* )
     echo $f
     switch ($f)
 	# these three go in the blat subdirectory
 	case ${DESTDIR}${BINDIR}/blat:
 	case ${DESTDIR}${BINDIR}/gfClient:
 	case ${DESTDIR}${BINDIR}/gfServer:
+	case ${DESTDIR}${BINDIR}/isPcr:
 	    ssh -n qateam@hgdownload "rm /mirrordata/apache/htdocs/admin/exe/$BINDIR/blat/$f:t"
 	    scp -p $f qateam@hgdownload:/mirrordata/apache/htdocs/admin/exe/$BINDIR/blat/$f:t
 	    ssh -n qateam@genome-euro "rm /mirrordata/apache/htdocs/admin/exe/$BINDIR/blat/$f:t"
 	    scp -p $f qateam@genome-euro:/mirrordata/apache/htdocs/admin/exe/$BINDIR/blat/$f:t
 	    breaksw
 	default:
 	    ssh -n qateam@hgdownload "rm /mirrordata/apache/htdocs/admin/exe/$BINDIR/$f:t"
 	    scp -p $f qateam@hgdownload:/mirrordata/apache/htdocs/admin/exe/$BINDIR/$f:t
 	    ssh -n qateam@genome-euro "rm /mirrordata/apache/htdocs/admin/exe/$BINDIR/$f:t"
 	    scp -p $f qateam@genome-euro:/mirrordata/apache/htdocs/admin/exe/$BINDIR/$f:t
 	    breaksw
     endsw
   end
 endif
 
 echo "userApps $MACHTYPE built on $HOST and scp'd to hgdownload and genome-euro [${0}: START=${ScriptStart} END=`date`]"
 
 exit 0