060c692dfeda837e9fd0385123f75abbf378ceb7 hiram Thu Sep 30 12:07:23 2021 -0700 add download file for repeatMasker.out.gz results no redmine diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh index 38df94c..19df450 100755 --- src/hg/utils/automation/asmHubTrackDb.sh +++ src/hg/utils/automation/asmHubTrackDb.sh @@ -162,30 +162,39 @@ bigDataUrl bbi/%s.tandemDups.bb type bigBed 12\n\n" "${asmId}" fi $scriptDir/asmHubTanDups.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.tanDups.html fi export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true` # see if there are repeatMasker bb files export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true` if [ "${rmskCount}" -gt 0 ]; then + +if [ ! -s "$buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz" ]; then + printf "ERROR: can not find trackData/repeatMasker/$asmId.sorted.fa.out.gz\n" 1>&2 + exit 255 +fi + +rm -f $buildDir/$asmId.repeatMasker.out.gz +ln -s trackData/repeatMasker/$asmId.sorted.fa.out.gz $buildDir/$asmId.repeatMasker.out.gz + printf "track repeatMasker compositeTrack on shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility dense type bigBed 6 + colorByStrand 50,50,150 150,50,50 maxWindowToDraw 10000000 spectrum on html html/%s.repeatMasker\n\n" "${asmId}" $scriptDir/asmHubRmsk.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt > $buildDir/html/$asmId.repeatMasker.html fi if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb ]; then