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--- a/Makefile.am 2023-04-21 19:13:21.119884090 +0530
+++ b/Makefile.am 2023-04-21 19:10:37.533407100 +0530
@@ -23,16 +23,17 @@
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\" $(AM_CFLAGS)
+bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(pkgdatadir)\/models\" $(AM_CFLAGS)
bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
# process scripts
-# treat tRNAscan-SE.conf as a script since it's just easier
-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE
+# config file
+dist_sysconf_DATA = tRNAscan-SE.conf
# for a few files, need to substitute perl path, bin directory, and lib directory
# first, define a function for it
-do_subst = sed -e 's,\@bindir\@,$(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,\@pkgdatadir\@,$(pkgdatadir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' -e 's,\@sysconfdir\@,$(sysconfdir),g'
# extra steps for cleaning/distribution
CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
@@ -51,15 +52,15 @@
bin/sstofa: src/sstofa.in Makefile
$(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa
- chmod +x bin/sstofa
+ if [ -x bin/sstofa ] ; then chmod +x bin/sstofa ; fi
bin/fasta2gsi: src/fasta2gsi.in Makefile
$(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi
- chmod +x bin/fasta2gsi
+ if [ -x bin/fasta2gsi ] ; then chmod +x bin/fasta2gsi ; fi
bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile
$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
- chmod +x bin/EukHighConfidenceFilter
+ if [ -x bin/EukHighConfidenceFilter ] ; then chmod +x bin/EukHighConfidenceFilter ; fi
bin/MitoHighConfidenceFilter: MitoHighConfidenceFilter.in Makefile
$(do_subst) < $(srcdir)/MitoHighConfidenceFilter.in > bin/MitoHighConfidenceFilter
@@ -67,11 +68,9 @@
# 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
+ test -d $(DESTDIR)/$(pkgdatadir) || mkdir -p $(DESTDIR)/$(pkgdatadir)
+ chmod u+w $(DESTDIR)/$(pkgdatadir)
+ cp -rf $(srcdir)/lib/* $(DESTDIR)/$(pkgdatadir)
# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files
uninstall-hook:
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