Program transform name

* Proper installation with prefix/suffix to program names * mummerplot fixes. Work with (almost) any terminal types. Not limited to ps and png anymore. Use interactive terminal by default.
mummer4 · Nov 26, 2024 · 61d2b1f · 61d2b1f
1 parent a16122b
commit 61d2b1f
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Showing 6 changed files with 218 additions and 148 deletions.
diff --git a/Makefile.am b/Makefile.am
@@ -157,14 +157,52 @@ EXTRA_DIST         += $(patsubst %,scripts/%.sh,$(shell_scripts))
 CLEANFILES         += $(libs_scripts) $(all_scripts)
 
 # Rules to generate the scripts, in .libs and in build directory.
+mummername      = $(shell echo mummer | sed '$(transform)')
+nucmername      = $(shell echo nucmer | sed '$(transform)')
+mgapsname       = $(shell echo mgaps | sed '$(transform)')
+prenucname      = $(shell echo prenuc | sed '$(transform)')
+postnucname     = $(shell echo postnuc | sed '$(transform)')
+preproname      = $(shell echo prepro | sed '$(transform)')
+postproname     = $(shell echo postpro | sed '$(transform)')
+showcoordsname  = $(shell echo show-coords | sed '$(transform)')
+showdiffname    = $(shell echo show-diff | sed '$(transform)')
+showsnpsname    = $(shell echo show-snps | sed '$(transform)')
+deltafiltername = $(shell echo delta-filter | sed '$(transform)')
+repeatmatchname = $(shell echo repeat-match | sed '$(transform)')
+
+
 script_inst_subst  = sed -e 's,[@]PERL[@],$(PERL),g' \
-                       -e 's,[@]BIN_DIR[@],$(bindir),g' \
-                       -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
-	               -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g'
+                         -e 's,[@]BIN_DIR[@],$(bindir),g' \
+                         -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
+                         -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g' \
+                         -e 's,[@]MUMMER[@],$(mummername),g' \
+                         -e 's,[@]MGAPS[@],$(mgapsname),g' \
+                         -e 's,[@]PRENUC[@],$(prenucname),g' \
+                         -e 's,[@]POSTNUC[@],$(postnucname),g' \
+                         -e 's,[@]PREPRO[@],$(preproname),g' \
+                         -e 's,[@]POSTPRO[@],$(postproname),g' \
+                         -e 's,[@]SHOWCOORDS[@],$(showcoordsname),g' \
+                         -e 's,[@]SHOWDIFF[@],$(showdiffname),g' \
+                         -e 's,[@]SHOWSNPS[@],$(showsnpsname),g' \
+                         -e 's,[@]NUCMER[@],$(nucmername),g' \
+                         -e 's,[@]DELTAFILTER[@],$(deltafiltername),g' \
+                         -e 's,[@]REPEATMATCH[@],$(repeatmatchname),g'
 script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
-                       -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
-                       -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
-	               -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g'
+                         -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
+                         -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
+                         -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g' \
+                         -e 's,[@]MUMMER[@],mummer,g' \
+                         -e 's,[@]MGAPS[@],mgaps,g' \
+                         -e 's,[@]PRENUC[@],prenuc,g' \
+                         -e 's,[@]POSTNUC[@],postnuc,g' \
+                         -e 's,[@]PREPRO[@],prepro,g' \
+                         -e 's,[@]POSTPRO[@],postpro,g' \
+                         -e 's,[@]SHOWCOORDS[@],show-coords,g' \
+                         -e 's,[@]SHOWDIFF[@],show-diff,g' \
+                         -e 's,[@]SHOWSNPS[@],show-snps,g' \
+                         -e 's,[@]NUCMER[@],nucmer,g' \
+                         -e 's,[@]DELTAFILTER[@],delta-filter,g' \
+                         -e 's,[@]REPEATMATCH[@],repeat-match,g'
 
 .libs/%: scripts/%.pl
 	@mkdir -p $(dir $@) && $(script_inst_subst) < $< > $@
@@ -176,8 +214,8 @@ script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
 	$(AM_V_GEN)$(script_local_subst) < $< > $@ && chmod a+x $@
 
 # Supporting modules
-script_lib_SCRIPTS = scripts/Foundation.pm scripts/tandem-repeat.awk
-EXTRA_DIST += $(script_lib_SCRIPTS)
+script_lib_DATA = scripts/Foundation.pm scripts/tandem-repeat.awk
+EXTRA_DIST += $(script_lib_DATA)
 
 #######
 # umd #

diff --git a/scripts/dnadiff.pl b/scripts/dnadiff.pl
@@ -68,19 +68,19 @@
 
 my @DEPEND_INFO =
     (
-     "$BIN_DIR/delta-filter",
-     "$BIN_DIR/show-diff",
-     "$BIN_DIR/show-snps",
-     "$BIN_DIR/show-coords",
-     "$BIN_DIR/nucmer",
+     "$BIN_DIR/@DELTAFILTER@",
+     "$BIN_DIR/@SHOWDIFF@",
+     "$BIN_DIR/@SHOWSNPS@",
+     "$BIN_DIR/@SHOWCOORDS@",
+     "$BIN_DIR/@NUCMER@",
      "$SCRIPT_DIR/Foundation.pm"
      );
 
-my $DELTA_FILTER = "$BIN_DIR/delta-filter";
-my $SHOW_DIFF = "$BIN_DIR/show-diff";
-my $SHOW_SNPS = "$BIN_DIR/show-snps";
-my $SHOW_COORDS = "$BIN_DIR/show-coords";
-my $NUCMER = "$BIN_DIR/nucmer";
+my $DELTA_FILTER = "$BIN_DIR/@DELTAFILTER@";
+my $SHOW_DIFF = "$BIN_DIR/@SHOWDIFF@";
+my $SHOW_SNPS = "$BIN_DIR/@SHOWSNPS@";
+my $SHOW_COORDS = "$BIN_DIR/@SHOWCOORDS@";
+my $NUCMER = "$BIN_DIR/@NUCMER@";
 
 my $SNPBuff         = 20;            # required buffer around "good" snps
 my $OPT_Prefix      = "out";         # prefix for all output files

diff --git a/scripts/exact-tandems.sh b/scripts/exact-tandems.sh
@@ -8,6 +8,7 @@ matchlen=$2
 
 bindir="@BIN_DIR@"
 libdir="@LIB_DIR@"
+repeatmatch="${bindir}/@REPEATMATCH@"
 
 if [ -z "$filename" -o -z "$matchlen" ]; then
    echo "USAGE:  $0 <file> <min-match-len>"
@@ -17,7 +18,7 @@ fi
 #echo "Finding matches and tandem repeats"
 # Trick: pipe exit status of first command to exit at end of the pipeline
 exec 4>&1; { \
-    { $bindir/repeat-match -t -n $matchlen $filename; echo $? >&3; } | \
+    { "$repeatmatch" -t -n $matchlen $filename; echo $? >&3; } | \
         tail -n +3 | sort -k1n -k2n | awk -f $libdir/tandem-repeat.awk >&4; \
 } 3>&1 | exit `cat`