767f1be1b487090edbfa9d3653af4a3192b81b7d
hiram
  Thu Oct 31 15:36:28 2024 -0700
mistaken bash code in csh script refs #3468

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 5630072..31cef08 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1657,37 +1657,38 @@
 ln -s $liftOverDir/$over $gpLiftOverDir/$over
 _EOF_
       );
     if ($tDb !~ m/^GC/) {
       $bossScript->add(<<_EOF_
 mkdir -p $gbdbLiftOverDir
 rm -f $gbdbLiftOverDir/$over
 ln -s $liftOverDir/$over $gbdbLiftOverDir/$over
 hgAddLiftOverChain -minMatch=0.1 -multiple -path=$gbdbLiftOverDir/$over \\
   $tDb $qDb
 _EOF_
       );
     }
 
     $bossScript->add(<<_EOF_
-if [ -d "/data/tmp" ]; then
-  export TMPDIR="/data/tmp"
-elif [ -d "/scratch/tmp" ]; then
-  export TMPDIR="/scratch/tmp"
+unsetenv TMPDIR
+if ( -d "/data/tmp" ) then
+  setenv TMPDIR "/data/tmp"
+else if ( -d "/scratch/tmp" ) then
+  setenv TMPDIR "/scratch/tmp"
 else
-  export TMPDIR="/tmp"
-fi
+  setenv TMPDIR "/tmp"
+endif
 # Update (or create) liftOver/md5sum.txt with the new .over.chain.gz.
 if (-e $gpLiftOverDir/md5sum.txt) then
   set tmpFile = `mktemp -t tmpMd5.XXXXXX`
   csh -c "grep -v $over $gpLiftOverDir/md5sum.txt || true" > \$tmpFile
   md5sum $gpLiftOverDir/$over \\
   | sed -e 's\@$gpLiftOverDir/\@\@' >> \$tmpFile
   sort \$tmpFile > $gpLiftOverDir/md5sum.txt
   rm \$tmpFile
 else
   md5sum $gpLiftOverDir/$over | sed -e 's\@$gpLiftOverDir/\@\@' \\
 	> $gpLiftOverDir/md5sum.txt
 endif
 _EOF_
       );
   }