24447c2527a64414060fc472626c0ae6a64f673c
hiram
  Thu Dec 12 13:06:47 2019 -0800
correctly eliminate dead machines from the rsync copies refs #23891

diff --git src/hg/utils/automation/doCrispr.pl src/hg/utils/automation/doCrispr.pl
index 9bebf99..e400ce9 100755
--- src/hg/utils/automation/doCrispr.pl
+++ src/hg/utils/automation/doCrispr.pl
@@ -375,31 +375,31 @@
 		     "-o tmp/outOffs/\$(root1).tab" );
   &HgAutomate::makeGsub($runDir, $templateCmd);
 
   my $whatItDoes = "Compute spec scores.";
   my $bossScript = newBash HgRemoteScript("$runDir/runSpecScores.bash",
 		$paraHub, $runDir, $whatItDoes);
 
   &HgAutomate::verbose(1,
          "# preparing the specificity alignment cluster run\n");
   `touch "$runDir/para_hub_$paraHub"`;
 
   my $paraRun = &HgAutomate::paraRun();
   my $gensub2 = &HgAutomate::gensub2();
   $bossScript->add(<<_EOF_
 # preload the /dev/shm on each parasol node with the fasta and index
-parasol list machines | awk '{print \$1}' | sort -u | while read M
+parasol list machines | grep -v dead | awk '{print \$1}' | sort -u | while read M
 do
   ssh "\${M}" "rsync -a --stats ${indexDir}/$db.fa ${indexDir}/$db.fa.fai /dev/shm/crispr10K.$db/ || true" < /dev/null
 done
 # and the /dev/shm on this parasol hub
 rsync -a --stats ${indexDir}/$db.fa ${indexDir}/$db.fa.fai /dev/shm/crispr10K.$db/ < /dev/null
 ln -s /dev/shm/crispr10K.$db/$db.fa* ./
 
 $gensub2 jobNames.txt single gsub jobList
 $paraRun
 find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab
 printf "# Number of specScores: %d\\n" "`cat ../specScores.tab | wc -l`" 1>&2
 _EOF_
   );
   $bossScript->execute();
 } # doSpecScores