5078b92cebab8e340d4c0d68e6d9e02f49c8db45 Merge parents 24890e3 0a35a5a kate Wed Jul 5 14:23:36 2017 -0700 Resolving merge conflict diff --cc src/hg/lib/makefile index 8c37456,cc0f91b..521c690 --- src/hg/lib/makefile +++ src/hg/lib/makefile @@@ -1,152 -1,152 +1,152 @@@ kentSrc = ../.. include ../../inc/localEnvironment.mk include ../../inc/common.mk XINC = -I$(MYSQLINC) O = acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o \ affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o \ altGraphX.o ancientRref.o \ annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o \ annoStreamDb.o annoStreamDbFactorSource.o annoStreamWig.o \ api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o \ barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o \ baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o \ bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o \ bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o \ bigGenePred.o bigPsl.o bigTransMap.o bioImage.o \ blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\ cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o \ ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o \ celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o \ chainDb.o chainLink.o chainNet.o chainNetDbLoad.o \ chicken13kInfo.o chromBins.o chromAlias.o chr18deletions.o \ chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o \ clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o \ contigAcc.o coordConv.o \ cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o \ cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o \ cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o customComposite.o \ bedDetail.o cgiApoptosis.o customAdjacency.o \ customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o \ dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o \ dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o \ dv.o dvBed.o dvXref2.o \ easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o \ encode/encodeErge.o encode/encodeErgeHssCellLines.o \ encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o \ encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o \ encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o \ encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o \ encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o \ encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeTag.o \ encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o \ encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o \ encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o \ encode/wgEncodeGencodeUniProt.o \ encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o \ encode/wgEncodeCell.o \ encode/encodeExp.o \ encode3/encode2Manifest.o encode3/encode3Valid.o \ ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o \ est3.o estOrientInfo.o \ estPair.o exoFish.o expData.o expRecord.o exprBed.o factorSource.o \ fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o \ flyBase2004Xref.o \ flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o \ genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o \ geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o \ geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o \ genomeRangeTreeFile.o genomicDups.o \ genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o \ ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o \ growthCondition.o grp.o \ - gtexAse.o gtexBoxplot.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o \ - gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o \ + gtexAse.o gtexBoxplot.o gtexEqtlCluster.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o \ + gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o \ gwasCatalog.o hAnno.o haplotypes.o \ hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o \ hapmapSnps.o hapmapSnpsCombined.o \ hashJoin.o hCommon.o \ hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o \ hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o \ hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o \ - HInv.o hubConnect.o hui.o humanParalog.o \ + HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o \ imageClone.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o \ jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o \ jgiGene.o joinMixer.o \ kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o \ lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o \ llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o \ makeItemsItem.o mammalPsg.o mapSts.o mathWig.o \ mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o \ minChromSize.o minGeneInfo.o mrnaMisMatch.o \ mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o \ ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o \ orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o \ peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o \ pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o \ rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o \ refLink.o refSeqStatus.o \ rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o \ rmskAlign.o rmskJoined.o rmskOut2.o \ rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o \ rnaSecStr.o tfbsConsFactors.o \ roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o \ sage.o sageCounts.o sageExp.o samAlignment.o sample.o \ sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o \ scopDes.o scoredRef.o search.o sessionThumbnail.o sgdAbundance.o \ sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o \ snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o \ snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o \ spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o \ stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o \ stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o \ switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o \ sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o \ tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o \ taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o \ tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o \ trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o \ transRegCode.o transRegCodeCondition.o \ transRegCodeProbe.o txCluster.o txCommon.o txEdgeBed.o \ txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o \ validateGisaid.o variant.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o \ wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o \ wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o \ zdobnovSynt.o oreganno.o \ oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o \ alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o \ megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o ifeq (${GBROWSE}, 1) GBROWSE_D=-DGBROWSE else GBROWSE_D= endif %.o: %.c ${CC} ${COPT} ${CFLAGS} ${GBROWSE_D} ${LOWELAB_DEFS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $< ../../lib/$(MACHTYPE)/jkhgap.a: $(O) ar rcus ../../lib/$(MACHTYPE)/jkhgap.a $(O) jWestHeader.h: jWestHeader.html sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$$/\\n"/;' jWestHeader.html > jWestHeader.h jWestBanner.h: jWestBanner.html sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$$/\\n"/;' jWestBanner.html > jWestBanner.h web.o: jWestHeader.h jWestBanner.h clean: rm -f $(O); rm -f jWestHeader.h jWestBanner.h rm -f ../../lib/$(MACHTYPE)/jkhgap.a; ctags: ctags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c ../inc/encode/*.h ../lib/encode/*.c tags: etags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c ../inc/encode/*.h ../lib/encode/*.c test: cd tests && ${MAKE} test