Makefile_targets

# This file contains user-specified targets, i.e. collections of
# executables or directories that are related and are frequently
# rebuilt together.

# Be sure to add any new target to the .PHONY list to prevent any
# silent make problems.

.PHONY: everything all depend clean execs_size nolink dogtools
.PHONY: assembler layoutold augment closure fintools simtools utilities 454tools

all: everything

assembler: assemble assemble_alt layout ueberal tiled assisted reporting qcmarkup 
layoutold: layout
utilities: util
simtools:  simulation
fintools:  finishing
closure:   human_closure
augment:   augment_aligns
454tools:  AddAlignsToFlowInfo CallWithCutoffs DetermineAcceptedReads \
  EvaluateUniformity  FilterByConsecutive FilterByKey FilterByOverlap \
  FastaSizes LoadInfoFile MakeFastaSubset \
  MakeLookupTable NormalizeFlows ProximityAnalysis QueryLookupTable \
  RemoveShortReads Realign454 RightTrimA SortOutNames SummarizeRegion \
  TrimToAlign UpdateFlowInfo Wells2Flowb TrimByBad RightTrimB
solexaPipeline: text ExtractSolexaFasta FeudalSize ParamsByRead SolexaFilters QualsFromSolexa SolexaComputeMetrics SolexaComputePerfectAligns FastaSizes ShortQueryLookup ImperfectLookupTable BestAlignmentTable AlignParamsByRead SelectPassing ProcessChIPData CoverageHistFromAligns ComputeBiasFromIntensities ComputeRegionalSimilarity BiasPiles_Solexa ComputeImageMetrics AverageImageMetrics GetSolexaClusterSize AddSolexaClusterSizeMetric BiasPlotGC_Solexa PairedReadParamsByRead
dogtools:  dogMapping