src/hg/lib/makefile 1.393
1.393 2009/08/02 18:57:07 markd
allow more flexability in find SAMTools
Index: src/hg/lib/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/makefile,v
retrieving revision 1.392
retrieving revision 1.393
diff -b -B -U 1000000 -r1.392 -r1.393
--- src/hg/lib/makefile 27 Jul 2009 21:52:08 -0000 1.392
+++ src/hg/lib/makefile 2 Aug 2009 18:57:07 -0000 1.393
@@ -1,122 +1,117 @@
include ../../inc/common.mk
XINC = -I$(MYSQLINC)
-L += -lm $(MYSQLLIBS)
-ifeq (${USE_BAM},1)
- L += ${SAMPATH}/libbam.a
-endif
-
O = acemblyClass.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 atomDb.o axtInfo.o \
axtLib.o bactigPos.o bamFile.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o \
bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed12Source.o \
bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bioImage.o \
blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\
cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o \
ccdsInfo.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 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 \
customFactory.o customPp.o customTrack.o cutter.o cytoBand.o \
dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o \
dgv.o dless.o dnaMotifSql.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 \
ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o \
est3.o estOrientInfo.o \
estPair.o exoFish.o expData.o expRecord.o exprBed.o \
fbTables.o featureBits.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 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 ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o \
ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o \
growthCondition.o grp.o \
hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o \
hapmapSnps.o hapmapSnpsCombined.o \
hCommon.o \
hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o \
hgFindSpec.o hgFindSpecCustom.o \
hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o \
HInv.o hui.o humanParalog.o \
imageClone.o isochores.o ispyTables.o itemAttr.o itemConf.o jalview.o \
jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o \
jgiGene.o \
kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o \
ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o \
llaInfo.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o mammalPsg.o mapSts.o \
mcnBreakpoints.o metaChromGraph.o microarray.o \
minChromSize.o minGeneInfo.o mrnaMisMatch.o \
mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o \
netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o \
pal.o pbStamp.o pcrResult.o pepPred.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 rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o \
rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.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 retroMrnaInfo.o \
roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o sample.o \
sqlProg.o tfbsCons.o tfbsConsSites.o \
sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o \
scopDes.o scoredRef.o sgdAbundance.o \
sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o \
snp.o snp125.o snp125CodingCoordless.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o \
snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o \
spDb.o splignAlign.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 \
switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o \
tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o \
taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o \
tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o \
trackDbCustom.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 \
validateGisaid.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 zdobnovSynt.o oreganno.o \
oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o
ifeq (${GBROWSE}, 1)
GBROWSE_D=-DGBROWSE
else
GBROWSE_D=
endif
%.o: %.c
${CC} ${COPT} ${CFLAGS} ${GBROWSE_D} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
../../lib/$(MACHTYPE)/jkhgap.a: $(O)
ar rcus ../../lib/$(MACHTYPE)/jkhgap.a $(O)
clean:
rm -f $(O);
rm -f ../../lib/$(MACHTYPE)/jkhgap.a;
ctags:
ctags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c
tags:
etags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c
test:
cd tests && ${MAKE} test