--- Makefile.am.orig	2017-12-03 07:00:58 UTC
+++ Makefile.am
@@ -8,8 +8,8 @@
 AUTOMAKE_OPTIONS = foreign subdir-objects
 
 # set flags
-AM_CFLAGS = -O
-LDADD = -lm
+#AM_CFLAGS = -O
+#LDADD = -lm
 
 # macros for program dependencies
 EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c
@@ -23,20 +23,21 @@ COVESRC = src/align.c src/dbviterbi.c sr
 bin_PROGRAMS = bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE
 bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND)
 bin_trnascan_1_4_SOURCES = src/trnascan.c
-bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
+bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(datadir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
 bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
 bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
 
 # process scripts
 # treat tRNAscan-SE.conf as a script since it's just easier
-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE
+sysconf_DATA = tRNAscan-SE.conf
 # for a few files, need to substitute perl path, bin directory, and lib directory
 # first, define a function for it
-do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(libdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' 
+do_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' 
 
 # extra steps for cleaning/distribution
 CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
-include_HEADERS = $(srcdir)/src/*.h 
+#include_HEADERS = $(srcdir)/src/*.h 
 EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter MitoHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src 
 
 # then create build rules
@@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf
 	$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
 	chmod +x bin/EukHighConfidenceFilter
 
-# copy libraries. We don't have "libraries" in the libgmp.so.4 kind, but we do have data libraries, so we don't have to deal with lib_LTLIBRARIES.
-install-data-hook:
-	chmod u+w $(exec_prefix)
-	test -d $(libdir) || mkdir $(libdir)
-	chmod u+w $(libdir)
-	test -d $(libdir)/tRNAscan-SE || mkdir $(libdir)/tRNAscan-SE
-	cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE 
-
-# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files 
-uninstall-hook:
-	chmod -R u+w $(libdir)/tRNAscan-SE
-	rm -rf $(libdir)/tRNAscan-SE
-
+gcodedir = $(pkgdatadir)/gcode
+modelsdir = $(pkgdatadir)/models
+modulesdir = $(pkgdatadir)/tRNAscanSE
+dist_gcode_DATA = lib/gcode/*
+dist_models_DATA = lib/models/*
+dist_modules_DATA = lib/tRNAscanSE/*