1## Makefile.am 2## tRNAscan-SE 3## 4## Settings for generating Makefile.in 5 6# not a GNU package 7# build object files in their source location 8AUTOMAKE_OPTIONS = foreign subdir-objects 9 10# set flags 11#AM_CFLAGS = -O 12#LDADD = -lm 13 14# macros for program dependencies 15EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c 16SQUIDUTILS = src/seqstat_main.c src/reformat_main.c src/shuffle_main.c src/revcomp_main.c src/getopt.c 17SQUIDSRC = src/alignio.c src/sqerror.c src/sqio.c src/iupac.c src/msf.c src/revcomp.c src/selex.c src/sre_ctype.c src/sre_math.c src/sre_string.c src/stack.c src/types.c src/gnuregex.c src/interleaved.c src/getopt.c 18SQUIDHDRS = src/squid.h src/sqfuncs.h src/gnuregex.h 19COVEMAIN = src/align_main.c src/build_main.c src/emit_main.c src/learnprior_main.c src/train_main.c src/scan_main.c src/score_main.c src/structcheck_main.c 20COVESRC = src/align.c src/dbviterbi.c src/debug.c src/emit.c src/fast-dbviterbi.c src/fastmodelmaker.c src/konings.c src/lengthdist.c src/maxmodelmaker.c src/misc.c src/model.c src/modelmaking.c src/prior.c src/probify.c src/save.c src/smallviterbi.c src/scorestack.c src/structs.c src/trace.c src/viterbi.c $(SQUIDSRC) 21 22# compile binaries 23bin_PROGRAMS = bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE 24bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND) 25bin_trnascan_1_4_SOURCES = src/trnascan.c 26bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(datadir)\/tRNAscan-SE\/models\" $(AM_CFLAGS) 27bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c 28bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c 29 30# process scripts 31# treat tRNAscan-SE.conf as a script since it's just easier 32dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE 33sysconf_DATA = tRNAscan-SE.conf 34# for a few files, need to substitute perl path, bin directory, and lib directory 35# first, define a function for it 36do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(datadir),g' -e 's,\@sysconfdir\@,$(sysconfdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' 37 38# extra steps for cleaning/distribution 39CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/* 40#include_HEADERS = $(srcdir)/src/*.h 41EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src 42 43# then create build rules 44 45tRNAscan-SE: tRNAscan-SE.src Makefile 46 $(do_subst) < $(srcdir)/tRNAscan-SE.src > tRNAscan-SE 47 chmod +x tRNAscan-SE 48 49tRNAscan-SE.conf: tRNAscan-SE.conf.src Makefile 50 $(do_subst) < $(srcdir)/tRNAscan-SE.conf.src > tRNAscan-SE.conf 51 chmod +x tRNAscan-SE.conf 52 53bin/sstofa: src/sstofa.in Makefile 54 $(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa 55 chmod +x bin/sstofa 56 57bin/fasta2gsi: src/fasta2gsi.in Makefile 58 $(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi 59 chmod +x bin/fasta2gsi 60 61bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile 62 $(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter 63 chmod +x bin/EukHighConfidenceFilter 64 65gcodedir = $(pkgdatadir)/gcode 66modelsdir = $(pkgdatadir)/models 67modulesdir = $(pkgdatadir)/tRNAscanSE 68dist_gcode_DATA = lib/gcode/* 69dist_models_DATA = lib/models/* 70dist_modules_DATA = lib/tRNAscanSE/* 71