obitools/ecoprimers
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some patches to compile on linux

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@205 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-04-23 22:22:27 +00:00
parent c36bc5e838
commit 796274d746
4 changed files with 9 additions and 8 deletions
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6
src/Makefile
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@ -6,7 +6,7 @@ PRIMER_OBJ= $(patsubst %.c,%.o,$(PRIMER_SRC))
SRCS= $(PRIMER_SRC) SRCS= $(PRIMER_SRC)
LIB= -lecoPCR -lecoprimer -lz -lm LIB= -lecoprimer -lecoPCR -lz -lm
LIBFILE= libecoPCR/libecoPCR.a \ LIBFILE= libecoPCR/libecoPCR.a \
libecoprimer/libecoprimer.a libecoprimer/libecoprimer.a
@ -26,7 +26,7 @@ all: $(EXEC)
# executable compilation and link # executable compilation and link
ecoPrimer: $(PRIMER_OBJ) $(LIBFILE) ecoPrimer: $(PRIMER_OBJ) $(LIBFILE)
$(CC) $(LDFLAGS) -O5 -m64 -fast -o $@ $< $(LIBPATH) $(LIB) $(CC) $(LDFLAGS) -O5 -m64 -o $@ $< $(LIBPATH) $(LIB)
######## ########
@ -55,4 +55,4 @@ clean:
$(MAKE) -C libecoprimer clean $(MAKE) -C libecoprimer clean

4
src/global.mk
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@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $< MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
CC=gcc CC=gcc
CFLAGS= -W -Wall -O5 -m64 -fast -g CFLAGS= -W -Wall -O5 -m64
#CFLAGS= -W -Wall -O0 -m64 -g #CFLAGS= -W -Wall -O0 -m64 -g
#CFLAGS= -W -Wall -O5 -fast -g #CFLAGS= -W -Wall -O5 -fast -g
@ -17,4 +17,4 @@ default: all
@sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \ @sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \
rm -f $*.d; [ -s $@ ] || rm -f $@ rm -f $*.d; [ -s $@ ] || rm -f $@
include $(SRCS:.c=.P) include $(SRCS:.c=.P)

3
src/libecoPCR/ecofilter.c
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@ -16,4 +16,5 @@ int eco_is_taxid_included( ecotaxonomy_t *taxonomy,
return 1; return 1;
return 0; return 0;
} }

4
src/libecoprimer/aproxpattern.c
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@ -39,8 +39,8 @@ ppattern_t buildPatternFromWord(word_t word, uint32_t patlen)
} }
#ifdef IS_UPPER(c) #ifdef IS_UPPER
#undef IS_UPPER(c) #undef IS_UPPER
#endif #endif
/* -------------------------------------------- */ /* -------------------------------------------- */