diff options
Diffstat (limited to 'sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch')
| -rw-r--r-- | sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch | 140 |
1 files changed, 140 insertions, 0 deletions
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch new file mode 100644 index 000000000000..acf3c2a6d862 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch @@ -0,0 +1,140 @@ +--- a/Makefile ++++ b/Makefile +@@ -20,9 +20,9 @@ + PERLBIN = perl + + ## where you want things installed +-BINDIR = $(HOME)/bin +-LIBDIR = $(HOME)/lib/tRNAscan-SE +-MANDIR = $(HOME)/man ++BINDIR = $(EPREFIX)/usr/bin ++LIBDIR = $(EPREFIX)/usr/share/trnascan-se ++MANDIR = $(EPREFIX)/usr/share/man + + ## NOTE !! If you later manually move the location of + ## binaries or data files in the BINDIR or LIBDIR directories, +@@ -33,10 +33,8 @@ + TEMPDIR = /tmp + + ## your compiler +-CC = gcc # GNU cc (if available) otherwise use vendor's cc + + ## any special compiler flags you want +-CFLAGS = -O # ok for most machines (remove -O for DEC OSF/1 cc compiler) + + ## machine specific definitions + # You shouldn't need any. The specific #define's in squid are historical. +@@ -58,7 +56,7 @@ + ####### + + SHELL = /bin/sh +-LIBS = -lm ++LIBS += -lm + .SUFFIXES : .c .o + + DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history +@@ -109,20 +107,20 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + +-trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++trnascan-1.4: trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c + + tRNAscan-SE: +- $(PERLDIR)/$(PERLBIN) checkversion.pl ++ $(PERLBIN) checkversion.pl + sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \ + sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \ + sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \ +@@ -200,11 +198,11 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c +- $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ + pavesi-NA.o $(SQUIDOBJ) $(LIBS) + + +@@ -220,7 +218,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -233,16 +231,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) + + ## other programs in Cove package (below) not needed for + ## tRNAscan-SE, but are included for users who wish to apply +@@ -255,25 +253,25 @@ + cp $(COVE_SUITE) $(BINDIR)/. + + covea: $(OBJ) align_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) + + coveb: $(OBJ) build_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) + + covee: $(OBJ) emit_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) + + covet: $(OBJ) train_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) + + covels: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) + + coves: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) + + structcheck: $(OBJ) structcheck_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) + + + ## Maspar memory limits |