debian/patches/fix_install_man.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
+Description: Fix installation of manpages
+
+--- a/Makefile
++++ b/Makefile
+@@ -60,8 +60,8 @@ install:
+ 	for file in $(PROGS) ; do\
+ 		cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
+ 	done
+-	for file in hmmer2 $(ls documentation/man/); do\
+-	   install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	for file in documentation/man/*.man ; do\
++	   install -D $$file $(MANDIR)/man$(MANSUFFIX)/`basename $$file .man`.$(MANSUFFIX);\
+ 	done
+ 
+ # Reverses the steps of "make install".  However, this should be handled

debian/patches/series

@@ -4,3 +4,4 @@ fix_typo.patch
 fix_install.patch
 hardening.patch
 #static_lib.patch
+fix_install_man.patch

debian/rules

@@ -33,12 +33,14 @@ override_dh_auto_install:
 	rename 's/^hmm(.+)2/hmm2$$1/;' $(CURDIR)/debian/tmp/bin/*
 	cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm(.+)2/hmm2$$1/;' *
 	cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm(.+)2/hmm2$$1/;' *
-	# mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1
+	rename 's/^hmm(.+)2/hmm2$$1/;' $(CURDIR)/debian/tmp/share/man/man1/*
+	mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1
 	# lkajan: resolve man page hypen issue:
 	sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/*
 
 override_dh_installexamples:
 	dh_installexamples
+	cd testsuite && make clean
 	mkdir -p $(sampledir);
 	sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
 	rm -f testsuite/*.ssi;