128037dded4246f2963b7ef08e8f4f1085a6c4eb hiram Thu May 7 14:51:38 2026 -0700 cron safe full path to hgsql refs #31811 diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh index 0b32546f4f9..e355b623c09 100755 --- src/hg/utils/automation/asmHubChainNetTrackDb.sh +++ src/hg/utils/automation/asmHubChainNetTrackDb.sh @@ -115,34 +115,34 @@ ln -s ../trackData/$lastzDir/axtChain/${accessionId}.${otherDb}.quickLink.bb $buildDir/quickLift/${otherDb}.link.bb else printf "# there is NO chainQuickLift${OtherDb}.bb\n" 1>&2 fi otherPrefix=`echo $otherDb | cut -c1-2` if [ "${otherPrefix}" = "GC" ]; then sciName=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *//i; s/ *(.*//;'` organism=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *.*(//i; s/).*//;'` taxId=`grep -i 'taxid:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*taxid: *//i;'` o_date=`grep -i 'date:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*date: *//i;'` matrix="" linGap="" minScore="" else - organism=`hgsql -N -e "select organism from dbDb where name=\"$otherDb\"" hgcentraltest` - sciName=`hgsql -N -e "select scientificName from dbDb where name=\"$otherDb\"" hgcentraltest` - taxId=`hgsql -N -e "select taxId from dbDb where name=\"$otherDb\"" hgcentraltest` - o_date=`hgsql -N -e "select description from dbDb where name=\"$otherDb\"" hgcentraltest` + organism=`/cluster/bin/x86_64/hgsql -N -e "select organism from dbDb where name=\"$otherDb\"" hgcentraltest` + sciName=`/cluster/bin/x86_64/hgsql -N -e "select scientificName from dbDb where name=\"$otherDb\"" hgcentraltest` + taxId=`/cluster/bin/x86_64/hgsql -N -e "select taxId from dbDb where name=\"$otherDb\"" hgcentraltest` + o_date=`/cluster/bin/x86_64/hgsql -N -e "select description from dbDb where name=\"$otherDb\"" hgcentraltest` matrix=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep matrix` minScore=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep MinScore` linGap=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep LinearGap` fi printf "############################################################################## # $otherDb - $organism - $sciName - taxId: $taxId ############################################################################## " printf "track chainNet$OtherDb compositeTrack on shortLabel $organism Chain/Net longLabel $organism ($o_date), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks