#--*- makefile -*--------------------------------------------------------------
#
#   Standard makefile
#
#------------------------------------------------------------------------------

# Path to project directory.
UPDIR = ..
# Path to subdirectories.
SUBDIR=

#
# Libraries and paths (which are not defined globally).
#

LIBS = -llocorna -l consensus2 -lsequence -lnumerics -ltools2
ifdef (concurrent)
LIBS += -ltbb
endif

LIB_PATH =
# -L. -L../lib
# ../lib/tbb/release

INC_PATH =
# -I. -I../../lib/tbb/include

#
# Objects and headers
#

SOURCES = fasta2maf.cc intervann.cc intervops.cc testbed.cc birthdayprobtest.cc maf2seq.cc filtermaf.cc MAFAlignment.cc MAFAlignmentTest.cc MAFAlignmentTools.cc MAFSearchTables.cc MAFSearchTables3.cc HashCorrelationFinder3.cc HashCorrelationFinderTest.cc InteractionClusterAnalyzer.cc LocoRnaMain.cc CorrelationTools.cc covarna.cc mafalignmenttest.cc LocoRnaParMain.cc covarnap.cc shufflemaf.cc locornamaintest.cc

OBJECTS = MAFAlignment.o MAFAlignmentTest.o MAFAlignmentTools.o MAFSearchTables.o MAFSearchTables3.o HashCorrelationFinder3.o HashCorrelationFinderTest.o InteractionClusterAnalyzer.o LocoRnaMain.o CorrelationTools.o LocoRnaParMain.o 

TARGETS = fasta2maf intervann intervops testbed birthdayprobtest maf2seq shufflemaf filtermaf covarna mafalignmenttest covarnap locornamaintest 

LIBRARY = liblocorna.a

#
# Install rule
#

compile: all

install: $(LIBRARY) $(TARGET)
	mv $(LIBRARY) $(UPDIR)/lib

#
# Call global Makefile to do the job.
#

include ../tools2/Makefile.global


