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