blob: ebfb2c7be7b888a04353dfe31f4f379b023f1bf6 (
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diff --git a/core/Makefile b/core/Makefile
index 8bb8baf..cf28559 100644
--- a/core/Makefile
+++ b/core/Makefile
@@ -1,5 +1,5 @@
PREFIX = /usr/local
-LIBDIR = $(PREFIX)/lib/mafft
+LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
BINDIR = $(PREFIX)/bin
MANDIR = $(PREFIX)/man/man1
@@ -127,136 +127,136 @@ mltaln.h : functions.h
touch mltaln.h
ord : $(OBJORD)
- $(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
tbfast : $(OBJTBFAST)
- $(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
tbfast2 : $(OBJTBFAST2)
- $(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
disttbfast : $(OBJDISTTBFAST)
- $(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
splittbfast : $(OBJSPLITTBFAST)
- $(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
splitfromaln : $(OBJSPLITFROMALN)
- $(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
splittbfast2 : $(OBJSPLITTBFAST2)
- $(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
dummy : $(OBJDUMMY)
- $(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
setcore : $(OBJSETCORE)
- $(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
countlen : $(OBJCOUNTLEN)
- $(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
seq2regtable : $(OBJSEQ2REGTABLE)
- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
regtable2seq : $(OBJREGTABLE2SEQ)
- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
f2cl : $(OBJF2CL)
- $(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
mccaskillwrap : $(OBJMCCASKILLWRAP)
- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
contrafoldwrap : $(OBJCONTRAFOLDWRAP)
- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
pairlocalalign : $(OBJPAIRLOCALALIGN)
- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
pairash : $(OBJPAIRASH)
- $(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
rnatest : $(OBJRNATEST)
- $(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
pair2hat3s : $(OBJPAIR2HAT3S)
- $(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
multi2hat3s : $(OBJMULTI2HAT3S)
- $(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
getlag : $(OBJGETLAG)
- $(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
tditr : $(OBJTDITR)
- $(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
dvtditr : $(OBJDVTDITR)
- $(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
mafft-profile : $(OBJGALN)
- $(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
gapfill : $(OBJGAPFILL)
- $(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
dndfast4 : $(OBJDNDFAST4)
- $(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
dndfast5 : $(OBJDNDFAST5)
- $(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
dndfast6 : $(OBJDNDFAST6)
- $(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
dndfast7 : $(OBJDNDFAST7)
- $(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
dndblast : $(OBJDNDBLAST)
- $(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
dndfast3 : $(OBJDNDFAST3)
- $(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
triplet : $(OBJTRIPLET)
- $(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
triplet3 : $(OBJTRIPLET3)
- $(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
sextet3 : $(OBJSEXTET3)
- $(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
sextet4 : $(OBJSEXTET4)
- $(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
sextet5 : $(OBJSEXTET5)
- $(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
mafft-distance : $(OBJDISTANCE)
- $(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
triplet5 : $(OBJTRIPLET5)
- $(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
triplet6 : $(OBJTRIPLET6)
- $(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
octet4 : $(OBJOCTET4)
- $(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
dndpre : $(OBJDNDPRE)
- $(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
dndpre2 : $(OBJDNDPRESCORE)
- $(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
score : $(OBJSCORE)
- $(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
genMtx : $(OBJGENMTX)
- $(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
+ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
gapfill.o : gapfill.c $(HEADER)
$(CC) $(CFLAGS) -c gapfill.c
|
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