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