Description: Fix script exe_paths
 denovo_map.pl and other stacks scripts hard-code the binary paths to the
 installation directory. However, we move these binaries to /usr/lib/stacks/bin,
 which breaks these scripts. This hard-codes the binary path to the correct
 location.
Author: Kevin Murray <spam@kdmurray.id.au>
Last-Update: 2016-10-21
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/Makefile.am
+++ b/Makefile.am
@@ -103,10 +103,10 @@ debug:
 	$(MAKE) all "CXXFLAGS=-g3 -Wall -DDEBUG -Og"
 
 install-data-hook:
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
+	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
 	mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl
 	chmod +x $(DESTDIR)$(bindir)/denovo_map.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
+	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
 	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
 	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
 	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
