28a32014fae85f167f805fe51e3eee91df731732 Merge parents e863249 0beae76 markd Fri Nov 4 14:48:45 2022 -0700 Merge branch 'master' into all-gencode-ranks diff --cc src/hg/lib/makefile index f65fa64,74ab364..b50f74c --- src/hg/lib/makefile +++ src/hg/lib/makefile @@@ -1,38 -1,38 +1,38 @@@ kentSrc = ../.. include ../../inc/localEnvironment.mk include ../../inc/common.mk XINC = -I$(MYSQLINC) O=adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o autoUpgrade.o axtInfo.o \ barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o \ bedDetail.o bigBedFind.o bigBedLabel.o bigDbSnp.o bigGenePred.o \ bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o \ cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o \ chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o \ chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o \ - customPp.o customTrack.o cv.o cytoBand.o dbDb.o defaultDb.o dnaMotifSql.o \ + customPp.o customTrack.o cv.o cytoBand.o dbDb.o defaultDb.o dnaMotifSql.o dupTrack.o \ encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o \ encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o \ encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o \ encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o \ - encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodePdb.o \ + encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o \ encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o \ encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o \ encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o \ estOrientInfo.o expData.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o \ - findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o \ + findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o \ genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o \ googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o \ gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o \ hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o \ hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o \ hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o \ jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o \ liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o \ microarray.o minChromSize.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o \ rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o \ sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o \ sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o \ tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o \ trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o \ variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o \