a71f33ea4a34a46a90957e9b59cd7235cbdff4e9 hiram Mon Aug 3 15:56:12 2026 -0700 adding annotation version notes correctly to ncbiGene.html description page refs #37958 diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl index 24dd3043425..009da4ce761 100755 --- src/hg/utils/automation/doAssemblyHub.pl +++ src/hg/utils/automation/doAssemblyHub.pl @@ -1965,38 +1965,40 @@ -maskedSeq=$buildDir/trackData/addMask/\$asmId.masked.2bit \$asmId) > do.log 2>&1 if [ -s "\$asmId.xenoRefGene.bb" ]; then bigBedInfo \$asmId.xenoRefGene.bb | egrep "^itemCount:|^basesCovered:" \\ | sed -e 's/,//g' > \$asmId.xenoRefGene.stats.txt LC_NUMERIC=en_US /usr/bin/printf "# xenoRefGene %s %'d %s %'d\\n" `cat \$asmId.xenoRefGene.stats.txt` | xargs echo fi else printf "# xenoRefGene step previously completed\\n" 1>&2 fi _EOF_ ); $bossScript->execute(); } # doXenoRefGene ######################################################################### -# * step: trackDb [workhorse] +# * step: trackDb [dbHost] sub doTrackDb { my $runDir = "$buildDir"; &HgAutomate::mustMkdir($runDir); my $whatItDoes = "construct asmId.trackDb.txt file"; + # must run on $dbHost: asmHubTrackDb.sh calls per-track html description + # generators (e.g. asmHubNcbiGene.pl) that hgsql the 'genark' database my $bossScript = newBash HgRemoteScript("$runDir/doTrackDb.bash", - $workhorse, $runDir, $whatItDoes); + $dbHost, $runDir, $whatItDoes); if (! -s "${buildDir}/trackData/chromAlias/${defaultName}.chromAlias.txt" ) { die "ERROR: can not find ${defaultName}.chromAlias.txt in\n# ${buildDir}/trackData/chromAlias/\n"; } $bossScript->add(<<_EOF_ export defaultName=$defaultName export asmId=$asmId export buildDir=$buildDir rm -f \$defaultName.chromAlias.txt ln -s trackData/chromAlias/\${defaultName}.chromAlias.txt . if [ -s trackData/chromAlias/\${defaultName}.chromAlias.bb ]; then rm -f \${defaultName}.chromAlias.bb ln -s trackData/chromAlias/\${defaultName}.chromAlias.bb .