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