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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts/Makefile @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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jpayne@69 1 #-- Imported variables from top level makefile
jpayne@69 2 # BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
jpayne@69 3
jpayne@69 4 ifndef BIN_DIR
jpayne@69 5 BIN_DIR := $(CURDIR)
jpayne@69 6 endif
jpayne@69 7 ifndef AUX_BIN_DIR
jpayne@69 8 AUX_BIN_DIR := $(CURDIR)
jpayne@69 9 endif
jpayne@69 10 ifndef SCRIPT_DIR
jpayne@69 11 SCRIPT_DIR := $(CURDIR)
jpayne@69 12 endif
jpayne@69 13
jpayne@69 14 SCRIPT_DIR := $(CURDIR)
jpayne@69 15 SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
jpayne@69 16 CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
jpayne@69 17 PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
jpayne@69 18 VPATH := $(BIN_DIR)
jpayne@69 19
jpayne@69 20 ALL := exact-tandems mapview mummerplot nucmer promer \
jpayne@69 21 run-mummer1 run-mummer3 nucmer2xfig dnadiff
jpayne@69 22
jpayne@69 23 #-- PHONY rules --#
jpayne@69 24 .PHONY: all clean
jpayne@69 25
jpayne@69 26
jpayne@69 27 all: $(ALL)
jpayne@69 28
jpayne@69 29
jpayne@69 30 clean:
jpayne@69 31 rm -f *~
jpayne@69 32 cd $(BIN_DIR); rm -f $(ALL)
jpayne@69 33
jpayne@69 34
jpayne@69 35
jpayne@69 36
jpayne@69 37 #-- not so PHONY rules --#
jpayne@69 38 exact-tandems: exact-tandems.csh
jpayne@69 39 $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69 40 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 41 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 42 exact-tandems.csh > $(BIN_DIR)/exact-tandems
jpayne@69 43 chmod 755 $(BIN_DIR)/exact-tandems
jpayne@69 44
jpayne@69 45 mapview: mapview.pl
jpayne@69 46 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 47 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 48 mapview.pl > $(BIN_DIR)/mapview
jpayne@69 49 chmod 755 $(BIN_DIR)/mapview
jpayne@69 50
jpayne@69 51 mummerplot: mummerplot.pl Foundation.pm
jpayne@69 52 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 53 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 54 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 55 mummerplot.pl > $(BIN_DIR)/mummerplot
jpayne@69 56 chmod 755 $(BIN_DIR)/mummerplot
jpayne@69 57
jpayne@69 58 dnadiff: dnadiff.pl Foundation.pm
jpayne@69 59 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 60 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 61 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 62 dnadiff.pl > $(BIN_DIR)/dnadiff
jpayne@69 63 chmod 755 $(BIN_DIR)/dnadiff
jpayne@69 64
jpayne@69 65 nucmer: nucmer.pl Foundation.pm
jpayne@69 66 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 67 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 68 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
jpayne@69 69 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 70 nucmer.pl > $(BIN_DIR)/nucmer
jpayne@69 71 chmod 755 $(BIN_DIR)/nucmer
jpayne@69 72
jpayne@69 73 promer: promer.pl Foundation.pm
jpayne@69 74 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 75 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69 76 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
jpayne@69 77 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 78 promer.pl > $(BIN_DIR)/promer
jpayne@69 79 chmod 755 $(BIN_DIR)/promer
jpayne@69 80
jpayne@69 81 run-mummer1: run-mummer1.csh
jpayne@69 82 $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69 83 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 84 run-mummer1.csh > $(BIN_DIR)/run-mummer1
jpayne@69 85 chmod 755 $(BIN_DIR)/run-mummer1
jpayne@69 86
jpayne@69 87 run-mummer3: run-mummer3.csh
jpayne@69 88 $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69 89 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69 90 run-mummer3.csh > $(BIN_DIR)/run-mummer3
jpayne@69 91 chmod 755 $(BIN_DIR)/run-mummer3
jpayne@69 92
jpayne@69 93 nucmer2xfig: nucmer2xfig.pl
jpayne@69 94 $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69 95 nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
jpayne@69 96 chmod 755 $(BIN_DIR)/nucmer2xfig