debian/patches/fix_main_makefile.patch

@@ -135,6 +135,24 @@
  
  forcelinks:
  	-rm $(LINKSTAMP)
+@@ -1676,7 +1624,7 @@ redo_links: clean_links
+ #********************************************************************************
+ 
+ header_libs:
+-	$(MAKE) -C HEADERLIBS all
++	echo "No headerlibs - just create libarb core" # $(MAKE) -C HEADERLIBS all
+ 
+ #********************************************************************************
+ 
+@@ -1708,7 +1656,7 @@ endif
+ 
+ 
+ binlink:
+-	$(MAKE) -C bin $(BIN_TARGET)
++	echo "No binaries, build library only" # $(MAKE) -C bin $(BIN_TARGET)
+ 
+ preplib:
+ 	(cd lib;$(MAKE) all)
 @@ -1728,7 +1676,7 @@ preplib:
  ifeq ($(WITHPERL),1)
  links_non_perl:	PERLTOOLS/PERLTOOLS.dummy
@@ -234,7 +252,27 @@
  	$(MAKE) build
  
  tarfile: rebuild
-@@ -1979,9 +1907,9 @@ arbapplications: nt pa e4 wetc pt na nal
+@@ -1914,7 +1842,8 @@ patch:
+ 
+ # test early whether save will work
+ savetest:
+-	@util/arb_srclst.pl >/dev/null
++	# @util/arb_srclst.pl >/dev/null
++	echo "No idea what util/arb_srclst.pl is doing - not in libarb source for Debian"
+ 
+ testsave: savetest
+ 
+@@ -1926,7 +1855,8 @@ save2: rmbak
+ 
+ save_test: rmbak
+ 	@echo "Testing source list.."
+-	@util/arb_srclst.pl > /dev/null
++	# @util/arb_srclst.pl > /dev/null
++	echo "No idea what util/arb_srclst.pl is doing - not in libarb source for Debian"
+ 
+ save_test_no_error:
+ 	@-$(MAKE) save_test
+@@ -1979,10 +1909,10 @@ arbapplications: nt pa e4 wetc pt na nal
  
  arb_external: convert tools gde readseq tg pst xmlin
  
@@ -242,11 +280,13 @@
 +arb_no_perl: arbapplications arb_external
  
 -arb: motif_xpm_hack
+-	$(MAKE) "WITHPERL=1" perl arb_no_perl
 +arb: 
- 	$(MAKE) "WITHPERL=1" perl arb_no_perl
++	$(MAKE) "WITHPERL=1" perl # arb_no_perl
  
  motif_xpm_hack:
-@@ -2121,7 +2049,6 @@ UNITS_TESTED = \
+ 	$(MAKE) -r -C "lib/motifHack" all
+@@ -2121,7 +2051,6 @@ UNITS_TESTED = \
  	SL/FAST_ALIGNER/FAST_ALIGNER.test \
  	SL/PRONUC/PRONUC.test \
  	WINDOW/libWINDOW.test \
@@ -254,12 +294,12 @@
  	CONVERTALN/CONVERTALN.test \
  	SL/SEQIO/SEQIO.test \
  	SL/PTCLEAN/PTCLEAN.test \
-@@ -2312,7 +2239,7 @@ post_commit_check:
+@@ -2312,7 +2241,7 @@ post_commit_check:
  # --------------------------------------------------------------------------------
  
  build: arb
 -	$(MAKE) binlink preplib compile_compatibility
-+	$(MAKE) core db SL/HELIX/HELIX.dummy
++	$(MAKE) core db SL/HELIX/HELIX.dummy SL/PTCLEAN/PTCLEAN.dummy
  
  all:
  	@echo "Build time" > $(TIMELOG)

debian/patches/ignore_unneeded_stuff.patch

@@ -171,32 +171,3 @@
  
  defined $short_version || die "expected known short_version!";
  defined $revision || die "expected known revision!";
---- a/Makefile
-+++ b/Makefile
-@@ -1624,7 +1624,7 @@ redo_links: clean_links
- #********************************************************************************
- 
- header_libs:
--	$(MAKE) -C HEADERLIBS all
-+	echo "No headerlibs - just create libarb core" # $(MAKE) -C HEADERLIBS all
- 
- #********************************************************************************
- 
-@@ -1656,7 +1656,7 @@ endif
- 
- 
- binlink:
--	$(MAKE) -C bin $(BIN_TARGET)
-+	echo "No binaries, build library only" # $(MAKE) -C bin $(BIN_TARGET)
- 
- preplib:
- 	(cd lib;$(MAKE) all)
-@@ -1910,7 +1910,7 @@ arb_external: convert tools gde readseq
- arb_no_perl: arbapplications arb_external
- 
- arb: 
--	$(MAKE) "WITHPERL=1" perl arb_no_perl
-+	$(MAKE) "WITHPERL=1" perl # arb_no_perl
- 
- motif_xpm_hack:
- 	$(MAKE) -r -C "lib/motifHack" all