5e98a4b579ae9b7efbcc20c0314b7b51e88b7caf hiram Mon May 29 12:13:19 2023 -0700 do not look for a database when it is an assembly hub (hs1) refs #31342 diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl index ed20aed..08e2ef7 100755 --- src/hg/utils/automation/doNcbiRefSeq.pl +++ src/hg/utils/automation/doNcbiRefSeq.pl @@ -984,31 +984,33 @@ die "ERROR: can not find /hive/data/genomes/$db/bed/idKeys/$db.idKeys.txt\n\t need to run doIdKeys.pl for $db before this procedure."; } # Force debug and verbose until this is looking pretty solid: # $opt_debug = 1; # $opt_verbose = 3 if ($opt_verbose < 3); # Establish what directory we will work in. my $date = `date +%Y-%m-%d`; chomp $date; $buildDir = $opt_buildDir ? $opt_buildDir : "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild/ncbiRefSeq.$date"; # may be working on a 2bit file that does not have a database browser $dbExists = 0; +if (! $opt_assemblyHub) { $dbExists = 1 if (&HgAutomate::databaseExists($dbHost, $db)); +} # Do everything. $stepper->execute(); $secondsEnd = `date "+%s"`; chomp $secondsEnd; my $elapsedSeconds = $secondsEnd - $secondsStart; my $elapsedMinutes = int($elapsedSeconds/60); $elapsedSeconds -= $elapsedMinutes * 60; # Tell the user anything they should know. my $stopStep = $stepper->getStopStep(); my $upThrough = ($stopStep eq 'cleanup') ? "" : " (through the '$stopStep' step)";