diff options
Diffstat (limited to 'sci-biology/mummer/files/mummer-3.23-fix-build-system.patch')
| -rw-r--r-- | sci-biology/mummer/files/mummer-3.23-fix-build-system.patch | 397 |
1 files changed, 397 insertions, 0 deletions
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch new file mode 100644 index 000000000000..b92f75c07719 --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch @@ -0,0 +1,397 @@ +Fix build system to restore some sanity + +--- a/Makefile ++++ b/Makefile +@@ -27,31 +27,27 @@ + + + TOP_DIR := $(CURDIR) +-BIN_DIR := $(TOP_DIR) +-AUX_BIN_DIR := $(TOP_DIR)/aux_bin ++ ++BIN_DIR = $(EPREFIX)/usr/bin ++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts ++AUX_BIN_DIR = $(EPREFIX)/usr/bin + + DOC_DIR := $(TOP_DIR)/docs + SCRIPT_DIR := $(TOP_DIR)/scripts + TIGR_SRC_DIR := $(TOP_DIR)/src/tigr + KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz + +-CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) +-CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) + SED := $(filter /%,$(shell /bin/sh -c 'type sed')) + CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) + PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-AR := $(filter /%,$(shell /bin/sh -c 'type ar')) + +-CXXFLAGS = -O3 +-CFLAGS = -O3 +-LDFLAGS = + + FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog + + + + #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES +-export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS ++export BIN_DIR SCRIPT_DIR AUX_BIN_DIR + + + +@@ -114,15 +110,15 @@ + + + kurtz: +- cd $(KURTZ_SRC_DIR); $(MAKE) mummer ++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer + + + scripts: +- cd $(SCRIPT_DIR); $(MAKE) all ++ $(MAKE) -C $(SCRIPT_DIR) all + + + tigr: +- cd $(TIGR_SRC_DIR); $(MAKE) all ++ $(MAKE) -C $(TIGR_SRC_DIR) all + + + uninstall: clean +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,21 +1,10 @@ +-#-- Imported variables from top level makefile +-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS ++BIN_DIR = $(EPREFIX)/usr/bin ++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts ++AUX_BIN_DIR = $(EPREFIX)/usr/bin + +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +-ifndef AUX_BIN_DIR +-AUX_BIN_DIR := $(CURDIR) +-endif +-ifndef SCRIPT_DIR +-SCRIPT_DIR := $(CURDIR) +-endif +- +-SCRIPT_DIR := $(CURDIR) + SED := $(filter /%,$(shell /bin/sh -c 'type sed')) + CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) + PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-VPATH := $(BIN_DIR) + + ALL := exact-tandems mapview mummerplot nucmer promer \ + run-mummer1 run-mummer3 nucmer2xfig dnadiff +@@ -39,58 +28,49 @@ + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- exact-tandems.csh > $(BIN_DIR)/exact-tandems +- chmod 755 $(BIN_DIR)/exact-tandems ++ exact-tandems.csh > exact-tandems + + mapview: mapview.pl + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- mapview.pl > $(BIN_DIR)/mapview +- chmod 755 $(BIN_DIR)/mapview ++ mapview.pl > mapview + + mummerplot: mummerplot.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- mummerplot.pl > $(BIN_DIR)/mummerplot +- chmod 755 $(BIN_DIR)/mummerplot ++ mummerplot.pl > mummerplot + + dnadiff: dnadiff.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- dnadiff.pl > $(BIN_DIR)/dnadiff +- chmod 755 $(BIN_DIR)/dnadiff ++ dnadiff.pl > dnadiff + + nucmer: nucmer.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- nucmer.pl > $(BIN_DIR)/nucmer +- chmod 755 $(BIN_DIR)/nucmer ++ nucmer.pl > nucmer + + promer: promer.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- promer.pl > $(BIN_DIR)/promer +- chmod 755 $(BIN_DIR)/promer ++ promer.pl > promer + + run-mummer1: run-mummer1.csh + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- run-mummer1.csh > $(BIN_DIR)/run-mummer1 +- chmod 755 $(BIN_DIR)/run-mummer1 ++ run-mummer1.csh > run-mummer1 + + run-mummer3: run-mummer3.csh + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- run-mummer3.csh > $(BIN_DIR)/run-mummer3 +- chmod 755 $(BIN_DIR)/run-mummer3 ++ run-mummer3.csh > run-mummer3 + + nucmer2xfig: nucmer2xfig.pl + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ +- nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig +- chmod 755 $(BIN_DIR)/nucmer2xfig ++ nucmer2xfig.pl > nucmer2xfig +--- a/src/kurtz/libbasedir/Makefile ++++ b/src/kurtz/libbasedir/Makefile +@@ -5,8 +5,6 @@ + + SPLINTFLAGS=-f ../Splintoptions -DDEBUG + +-LD=$(CC) +- + ##CFLAGS=${DEFINECFLAGS} + + LIBBASE=libbase.a +@@ -24,14 +22,14 @@ + + + $(LIBBASE): $(LIBOBJECTS) +- ar sruv $@ $(LIBOBJECTS) ++ $(AR) sruv $@ $(LIBOBJECTS) + + + include Filegoals.mf + + + $(LIBBASEDBG): $(LIBDEBUGOBJECTS) +- ar sruv $@ $(LIBDEBUGOBJECTS) ++ $(AR) sruv $@ $(LIBDEBUGOBJECTS) + + + .PHONY:clean +--- a/src/kurtz/Makefile ++++ b/src/kurtz/Makefile +@@ -1,7 +1,7 @@ + all: +- cd libbasedir; $(MAKE) all +- cd streesrc; $(MAKE) all +- cd mm3src; $(MAKE) all ++ $(MAKE) -C libbasedir all ++ $(MAKE) -C streesrc all ++ $(MAKE) -C mm3src all + + clean: + rm -f *~ +@@ -10,11 +10,11 @@ + cd mm3src; $(MAKE) clean + + mummer: +- cd libbasedir; $(MAKE) libbase.a +- cd streesrc; $(MAKE) libstree.a +- cd mm3src; $(MAKE) mummer ++ $(MAKE) -C libbasedir libbase.a ++ $(MAKE) -C streesrc libstree.a ++ $(MAKE) -C mm3src mummer + + splintall: +- cd libbasedir; ${MAKE} splintall +- cd streesrc; ${MAKE} splintall +- cd mm3src; ${MAKE} splintall ++ $(MAKE) -C libbasedir splintall ++ $(MAKE) -C streesrc splintall ++ $(MAKE) -C mm3src splintall +--- a/src/kurtz/mm3src/Makefile ++++ b/src/kurtz/mm3src/Makefile +@@ -3,11 +3,7 @@ + + ##include ../Makedef + +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +- +-VPATH := $(BIN_DIR) ++BIN_DIR = $(EPREFIX)/usr/bin + + ALL := maxmat3.x maxmat3.dbg.x + +@@ -15,11 +11,8 @@ + LIBSTREEDIR=../streesrc + INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR} + +-override CFLAGS+=$(INCLUDEDIR) +-##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR) +-##LDFLAGS=${DEFINELDFLAGS} ++override CPPFLAGS+=$(INCLUDEDIR) + SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG +-LD=$(CC) + + LIBBASE=$(LIBBASEDIR)/libbase.a + LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a +@@ -40,16 +33,16 @@ + all: $(ALL) + + mummer: $(MUM3OBJECTS) $(LIBSTREE) +- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ +- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ ++ -o $@ + + maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE) +- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ +- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ ++ -o $@ + + maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG) +- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ +- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ ++ -lm -o $@ + + include Filegoals.mf + +--- a/src/kurtz/streesrc/Makefile ++++ b/src/kurtz/streesrc/Makefile +@@ -23,8 +23,6 @@ + + #-DSTARTFACTOR=0.5 + +-LD=${CC} +- + LIBBASE=${LIBBASEDIR}/libbase.a + LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a + +@@ -65,29 +63,29 @@ + include Filegoals.mf + + libstree.4.a: $(OBJECTS4) +- ar sruv $@ $(OBJECTS4) ++ $(AR) sruv $@ $(OBJECTS4) + + libstree.a: $(OBJECTS) +- ar sruv $@ $(OBJECTS) ++ $(AR) sruv $@ $(OBJECTS) + + libstree.dbg.4.a: $(DBGOBJECTS4) +- ar sruv $@ $(DBGOBJECTS4) ++ $(AR) sruv $@ $(DBGOBJECTS4) + + libstree.dbg.a: $(DBGOBJECTS) +- ar sruv $@ $(DBGOBJECTS) ++ $(AR) sruv $@ $(DBGOBJECTS) + + + stree.x: stree.o libstree.a +- $(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ ++ $(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ + + loc.x: loc.o libstree.a +- $(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ ++ $(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ + + stree.dbg.x: stree.dbg.o libstree.dbg.a +- $(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ ++ $(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ + + loc.dbg.x: loc.dbg.o libstree.dbg.a +- $(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ ++ $(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ + + streeproto.h: $(PROTOFILES) Mkstreeproto.sh + @echo "make $@" +--- a/src/tigr/Makefile ++++ b/src/tigr/Makefile +@@ -1,20 +1,3 @@ +-#-- Imported variables from top level makefile +-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS +- +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +-ifndef AUX_BIN_DIR +-AUX_BIN_DIR := $(CURDIR) +-endif +- +-OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@ +-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ +- chmod 755 $(BIN_DIR)/$@ +-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ +- chmod 755 $(AUX_BIN_DIR)/$@ +-VPATH := $(AUX_BIN_DIR):$(BIN_DIR) +- + ALL := annotate combineMUMs delta-filter gaps mgaps \ + postnuc postpro prenuc prepro repeat-match \ + show-aligns show-coords show-tiling show-snps \ +@@ -38,59 +21,22 @@ + + #-- not so PHONY rules --# + delta.o: delta.cc delta.hh +- $(OBJ_RULE) +- + tigrinc.o: tigrinc.cc tigrinc.hh +- $(OBJ_RULE) +- + sw_align.o: sw_align.cc sw_align.hh tigrinc.hh +- $(OBJ_RULE) +- + translate.o: translate.cc translate.hh +- $(OBJ_RULE) +- + + annotate: annotate.cc tigrinc.o +- $(BIN_RULE) +- + combineMUMs: combineMUMs.cc tigrinc.o +- $(BIN_RULE) +- + delta-filter: delta-filter.cc tigrinc.o delta.o +- $(BIN_RULE) +- + gaps: gaps.cc tigrinc.o +- $(BIN_RULE) +- + mgaps: mgaps.cc tigrinc.o +- $(BIN_RULE) +- + postnuc: postnuc.cc tigrinc.o sw_align.o +- $(AUX_BIN_RULE) +- + postpro: postpro.cc tigrinc.o sw_align.o translate.o +- $(AUX_BIN_RULE) +- + prenuc: prenuc.cc tigrinc.o +- $(AUX_BIN_RULE) +- + prepro: prepro.cc tigrinc.o translate.o +- $(AUX_BIN_RULE) +- + repeat-match: repeat-match.cc tigrinc.o +- $(BIN_RULE) +- + show-aligns: show-aligns.cc tigrinc.o translate.o delta.o +- $(BIN_RULE) +- + show-coords: show-coords.cc tigrinc.o delta.o +- $(BIN_RULE) +- + show-tiling: show-tiling.cc tigrinc.o delta.o +- $(BIN_RULE) +- + show-snps: show-snps.cc tigrinc.o translate.o delta.o +- $(BIN_RULE) +- + show-diff: show-diff.cc tigrinc.o delta.o +- $(BIN_RULE) |