80ef5aceda1a2e29e3e1e654c8de191848405cda hiram Fri Apr 7 10:23:32 2023 -0700 tolerate ebiGene for HPRC project refs #30508 diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh index 726496f..3345310 100755 --- src/hg/utils/automation/asmHubTrackDb.sh +++ src/hg/utils/automation/asmHubTrackDb.sh @@ -815,30 +815,60 @@ priority 40 visibility pack color 150,0,0 type bigBed 12 . bigDataUrl bbi/%s.ensGene.bb searchIndex name searchTrix ixIxx/%s.ensGene.ix html html/%s.ensGene\n\n" "${ensVersion}" "${asmId}" "${asmId}" "${asmId}" $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}" else printf "# no ensGene found\n" 1>&2 fi +################################################################### +# Ensembl/ebiGene for HPRC project +if [ -d ${buildDir}/trackData/ebiGene ]; then + export ebiGeneBb=`ls ${buildDir}/trackData/ebiGene/*.bb 2> /dev/null || true | head -1` + if [ -s "${ebiGeneBb}" ]; then + export ebiGeneLink=`echo $ebiGeneBb | sed -e 's#.*trackData#../trackData#;'` + printf "# link: $ebiGeneLink ${buildDir}/bbi/${asmId}.ebiGene.bb\n" 1>&2 + rm -f ${buildDir}/bbi/${asmId}.ebiGene.bb + ln -s $ebiGeneLink ${buildDir}/bbi/${asmId}.ebiGene.bb + + printf "track ebiGene +shortLabel Ensembl v2 +longLabel Ensembl annotation v2 +group genes +visibility pack +color 150,0,0 +type bigGenePred +bigDataUrl bbi/%s.ebiGene.bb +searchIndex name,name2,txId,geneName,parentTranscript +labelFields name,name2,txId,geneName,parentTranscript +defaultLabelFields name +labelSeperator \" \" +html html/%s.ebiGene\n\n" "${asmId}" "${asmId}" + +# $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}" + fi + +fi + +################################################################### # hubLinks is for mouseStrains specific hub only export hubLinks="/hive/data/genomes/asmHubs/hubLinks" if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}" fi ## for mouse strain hubs only ## turned off 2022-11-02 until these can be correctly translated ## to GenArk naming schemes ### if [ -s "${buildDir}/$asmId.bigMaf.trackDb.txt" ]; then ### printf "include %s.bigMaf.trackDb.txt\n\n" "${asmId}" ### fi ################################################################### # check for blat sameSpecies liftOver, then link to lift over chain file export lo=`ls -d ${buildDir}/trackData/blat.* 2> /dev/null | wc -l`