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157 lines
5.1 KiB
157 lines
5.1 KiB
Makefile | 8 +++---
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scripts/Makefile | 6 +++-
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scripts/aln2wig/Makefile | 8 +++---
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scripts/compileSpliceCands/Makefile | 6 ++--
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src/Makefile | 43 ++++++++++++++++++----------------
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5 files changed, 38 insertions(+), 33 deletions(-)
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diff --git a/Makefile b/Makefile
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index e23a667..64610c8 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -3,9 +3,9 @@
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#
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all:
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- cd src && ${MAKE}
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- cd scripts && ${MAKE}
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+ $(MAKE) -C src
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+ $(MAKE) -C scripts
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clean:
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- cd src && ${MAKE} clean
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- cd scripts && ${MAKE} clean
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+ $(MAKE) -C src clean
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+ $(MAKE) -C scripts clean
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diff --git a/scripts/Makefile b/scripts/Makefile
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index 6d4dd67..ab6a885 100644
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--- a/scripts/Makefile
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+++ b/scripts/Makefile
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@@ -1,5 +1,7 @@
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all :
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- cd aln2wig && ${MAKE}
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+ $(MAKE) -C aln2wig
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+ $(MAKE) -C compileSpliceCands
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clean :
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- cd aln2wig && ${MAKE} clean
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+ $(MAKE) -C aln2wig clean
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+ $(MAKE) -C compileSpliceCands
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diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
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index 64d09f5..9752980 100644
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--- a/scripts/aln2wig/Makefile
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+++ b/scripts/aln2wig/Makefile
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@@ -1,10 +1,10 @@
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-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
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+CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
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psl2wig : aln2wig.o
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- gcc $(CFLAGS) -o aln2wig aln2wig.o;
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- cp aln2wig ../../bin
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
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+ cp aln2wig ../../bin/
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psl2wig.o : aln2wig.c
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- gcc $(CFLAGS) -c aln2wig.c
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+ $(CC) $(CFLAGS) -c aln2wig.c
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all : psl2wig
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diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
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index cddada5..8079791 100644
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--- a/scripts/compileSpliceCands/Makefile
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+++ b/scripts/compileSpliceCands/Makefile
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@@ -1,8 +1,8 @@
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compileSpliceCands : compileSpliceCands.o list.h list.o
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- gcc -o compileSpliceCands compileSpliceCands.o list.o;
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-# cp compileSpliceCands ../../bin
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
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+ cp compileSpliceCands ../../bin/
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compileSpliceCands.o : compileSpliceCands.c
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- gcc -Wall -pedantic -ansi -c compileSpliceCands.c
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+ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c
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all : compileSpliceCands
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diff --git a/src/Makefile b/src/Makefile
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index 71795b6..732b953 100644
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--- a/src/Makefile
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+++ b/src/Makefile
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@@ -6,8 +6,8 @@
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# a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
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# - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
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#
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-CC = g++
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-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static
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+CXX ?= g++
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+CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static
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INCLS = -I../include -I.
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LIBS = # -lcwd
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OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
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@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
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PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
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INFO = cflags
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-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
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+all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
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.SUFFIXES:
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.SUFFIXES: .cc .o .so
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.cc.o:
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- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
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+ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
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-augustus: augustus.cc $(OBJS) $(DUMOBJS)
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+bin: $(PROGR)
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+ cp $(PROGR) ../bin/
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+
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+augustus: augustus.o $(OBJS) $(DUMOBJS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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cp augustus ../bin/
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-etraining: etraining.cc $(TOBJS) $(OBJS)
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+etraining: etraining.o $(TOBJS) $(OBJS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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cp etraining ../bin/
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-evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+evaluate: evaluate.o $(OBJS) $(DUMOBJS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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-consensusFinder: consensusFinder.cc consensus.o
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+consensusFinder: consensusFinder.o consensus.o
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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-curve2hints: curve2hints.cc exon_seg.o
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+curve2hints: curve2hints.o exon_seg.o
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
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+fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
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types.o properties.o geneticcode.o pp_profile.o lldouble.o
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- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
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cp fastBlockSearch ../bin/
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-prepareAlign: pp_prepare_align.cc
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- $(CC) $(CFLAGS) -o $@ $^
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+prepareAlign: pp_prepare_align.o
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
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cp prepareAlign ../bin/
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info:
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- echo "$(CFLAGS)" > $(INFO)
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+ echo "$(CXXFLAGS)" > $(INFO)
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clean:
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- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
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+ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/*
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tidy: clean
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rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
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