533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/lib/makefile src/hg/lib/makefile index 438c461..f748bd4 100644 --- src/hg/lib/makefile +++ src/hg/lib/makefile @@ -1,169 +1,80 @@ 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 annoStreamDbPslPlus.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 bigBedLabel.o \ - bigDbSnp.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 cartEdit0.o cartEdit1.o cartJson.o cartTrackDb.o cartRewrite.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 \ - clinvarSub.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 dbSnpDetails.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/wgEncodeGencodeGeneSymbol.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 \ - facetedTable.o facetField.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 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 hic.o hicUi.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o \ - HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o hubPublic.o \ - imageClone.o indelShift.o interact.o interactUi.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 protobuf.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 seqWindow.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 trackDbCache.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o \ - transRegCode.o transRegCodeCondition.o \ - transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o \ - txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o \ - variant.o variantProjector.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 \ - gencodeAnnotationRemark.o gencodeAttrs.o gencodeToEntrezGene.o \ - gencodeExonSupport.o gencodeGeneSource.o gencodeToGeneSymbol.o gencodeToPdb.o \ - gencodeToPubMed.o gencodeToRefSeq.o gencodeTag.o \ - gencodeTranscriptionSupportLevel.o gencodeTranscriptSource.o \ - gencodeTranscriptSupport.o gencodeToUniProt.o - +O=adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o autoUpgrade.o axtInfo.o \ + barChartBed.o barChartUi.o bed.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 \ + 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/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 gcPercent.o genbank.o genbankBlackList.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 \ + 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 rikenCluster.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 \ + wiggleUtils.o wikiLink.o ifeq (${USE_HIC}, 1) O += straw.o endif 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 straw.o: straw/straw.cpp straw/straw.h straw/cStraw.cpp cd straw && ${MAKE} straw clean: rm -f $(O); rm -f jWestHeader.h jWestBanner.h rm -f ../../lib/$(MACHTYPE)/jkhgap.a; cd straw && ${MAKE} clean 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