eaea1cfa2424b5d3754e0a50df60fa53c5074125
hiram
  Mon May 24 10:24:49 2021 -0700
better cleaning and do not load up the Ranges table refs #27546

diff --git src/hg/utils/automation/doCrispr.pl src/hg/utils/automation/doCrispr.pl
index 883b498..e18b8da 100755
--- src/hg/utils/automation/doCrispr.pl
+++ src/hg/utils/automation/doCrispr.pl
@@ -530,31 +530,30 @@
 $python $crisprScripts/createBigBed.py $db allGuides.bed specScores.tab effScores.tab offtargets.offsets.tab
 _EOF_
   );
   if (!$forHub) {
     $bossScript->add(<<_EOF_
 # now link it into gbdb
 mkdir -p /gbdb/$db/$tableName/
 ln -sf `pwd`/crispr.bb /gbdb/$db/$tableName/crispr.bb
 ln -sf `pwd`/crisprDetails.tab /gbdb/$db/$tableName/crisprDetails.tab
 _EOF_
      );
   }
   if ($dbExists && !$forHub) {
     $bossScript->add(<<_EOF_
 hgBbiDbLink $db ${tableName}Targets /gbdb/$db/$tableName/crispr.bb
-hgLoadBed $db ${tableName}Ranges ranges/crisprRanges.bed
 _EOF_
     );
   }
   $bossScript->execute();
 } # doLoad
 
 #########################################################################
 # * step: cleanup [fileServer]
 sub doCleanup {
   my $runDir = "$buildDir";
   my $whatItDoes = "It cleans up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/doCleanup.bash", $fileServer,
 				      $runDir, $whatItDoes);
   # Verify previous step is complete
   #   it continue.
@@ -564,51 +563,53 @@
     }
     if ( -s "specScores/$db.fa.gz" ) {
      &HgAutomate::verbose(1,
          "# step cleanup is already completed, continuing...\n");
      return;
     }
   }
 
   $bossScript->add(<<_EOF_
 if [ -s "specScores/$db.fa.gz" ]; then
   printf "# step cleanup has already completed.\\n"
   exit 0
 fi
 printf "#\tdisk space before cleaning\\n"
 df -h .
-rm -fr ranges/tmp
-rm -fr guides/err
-rm -fr guides/tmp
-rm -f guides/batch.bak
-rm -f specScores/batch.bak
-rm -fr specScores/err
-rm -fr specScores/tmp
-rm -fr effScores/err
-rm -fr effScores/tmp
-rm -f effScores/batch.bak
-rm -fr offTargets/err
-rm -fr offTargets/tmp
-rm -f offTargets/batch.bak
-gzip specScores.tab effScores.tab offtargets.offsets.tab
-ssh $bigClusterHub parasol list machines | awk '{print \$1}' | sort -u | while read M
+rm -fr ranges/tmp &
+rm -fr ranges/ranges.fa &
+rm -fr guides/err &
+rm -fr guides/tmp &
+rm -f guides/batch.bak &
+rm -f specScores/batch.bak &
+rm -f specScores/$db.fa specScores/$db.fa.fai &
+rm -f indexFa/$db.fa indexFa/$db.fa.fai &
+rm -fr specScores/err &
+rm -fr specScores/tmp &
+rm -fr effScores/err &
+rm -fr effScores/tmp &
+rm -f effScores/batch.bak &
+rm -fr offTargets/err &
+rm -fr offTargets/tmp &
+rm -f offTargets/batch.bak &
+gzip specScores.tab effScores.tab offtargets.offsets.tab &
+wait
+ssh $bigClusterHub parasol list machines | grep -v dead | awk '{print \$1}' | sort -u | while read M
 do
   ssh "\${M}" "rm -fr /dev/shm/crispr10K.$db" < /dev/null
 done
 ssh $bigClusterHub "rm -fr /dev/shm/crispr10K.$db" < /dev/null
-rm -f specScores/$db.fa specScores/$db.fa.fai
-rm -f indexFa/$db.fa indexFa/$db.fa.fai
 printf "#\tdisk space after cleaning\\n"
 df -h .
 _EOF_
   );
   $bossScript->execute();
 } # doCleanup
 
 #########################################################################
 # main
 
 # Prevent "Suspended (tty input)" hanging:
 &HgAutomate::closeStdin();
 
 # Make sure we have valid options and exactly 1 argument:
 &checkOptions();