core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- 1 file changed, 50 insertions(+), 50 deletions(-) diff --git a/core/Makefile b/core/Makefile index 9acebb3..3838a45 100644 --- a/core/Makefile +++ b/core/Makefile @@ -145,151 +145,151 @@ mltaln.h : functions.h touch mltaln.h version : version.c mltaln.h - $(CC) -o $@ version.c $(MYCFLAGS) + $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) tbfast : $(OBJTBFAST) - $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) addsingle : $(OBJADDSINGLE) - $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) tbfast2 : $(OBJTBFAST2) - $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) disttbfast : $(OBJDISTTBFAST) - $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) makedirectionlist : $(OBJMAKEDIRECTIONLIST) - $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) splittbfast : $(OBJSPLITTBFAST) - $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) splitfromaln : $(OBJSPLITFROMALN) - $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) splittbfast2 : $(OBJSPLITTBFAST2) - $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) dummy : $(OBJDUMMY) - $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) setcore : $(OBJSETCORE) - $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) countlen : $(OBJCOUNTLEN) - $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) seq2regtable : $(OBJSEQ2REGTABLE) - $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) regtable2seq : $(OBJREGTABLE2SEQ) - $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) setdirection : $(OBJSETDIRECTION) - $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) replaceu : $(OBJREPLACEU) - $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) restoreu : $(OBJRESTOREU) - $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) f2cl : $(OBJF2CL) - $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) mccaskillwrap : $(OBJMCCASKILLWRAP) - $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) contrafoldwrap : $(OBJCONTRAFOLDWRAP) - $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) pairlocalalign : $(OBJPAIRLOCALALIGN) - $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) pairash : $(OBJPAIRASH) - $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) rnatest : $(OBJRNATEST) - $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) pair2hat3s : $(OBJPAIR2HAT3S) - $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) multi2hat3s : $(OBJMULTI2HAT3S) - $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) getlag : $(OBJGETLAG) - $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) tditr : $(OBJTDITR) - $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) dvtditr : $(OBJDVTDITR) - $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) mafft-profile : $(OBJGALN) - $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) gapfill : $(OBJGAPFILL) - $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) dndfast4 : $(OBJDNDFAST4) - $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) dndfast5 : $(OBJDNDFAST5) - $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) dndfast6 : $(OBJDNDFAST6) - $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) dndfast7 : $(OBJDNDFAST7) - $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) dndblast : $(OBJDNDBLAST) - $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) dndfast3 : $(OBJDNDFAST3) - $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) triplet : $(OBJTRIPLET) - $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) triplet3 : $(OBJTRIPLET3) - $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) sextet3 : $(OBJSEXTET3) - $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) sextet4 : $(OBJSEXTET4) - $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) sextet5 : $(OBJSEXTET5) - $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) mafft-distance : $(OBJDISTANCE) - $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) triplet5 : $(OBJTRIPLET5) - $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) triplet6 : $(OBJTRIPLET6) - $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) octet4 : $(OBJOCTET4) - $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) dndpre : $(OBJDNDPRE) - $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) dndpre2 : $(OBJDNDPRESCORE) - $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) score : $(OBJSCORE) - $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) genMtx : $(OBJGENMTX) - $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) gapfill.o : gapfill.c $(HEADER) $(CC) $(MYCFLAGS) -c gapfill.c @@ -525,7 +525,7 @@ install : all chmod 755 $(SCRIPTS) $(INSTALL) $(SCRIPTS) $(BINDIR) chmod 755 $(PROGS) - $(INSTALL) -s $(PROGS) $(LIBDIR) + $(INSTALL) $(PROGS) $(LIBDIR) $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) ( cd $(BINDIR); \