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785
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aaronmk
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##### Vars/functions
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1272
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aaronmk
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# Paths
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895
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aaronmk
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bin := ../bin
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1824
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aaronmk
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inputCoreMaps := DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv\
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1843
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aaronmk
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VegX-VegBIEN.stems.csv
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895
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aaronmk
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1824
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aaronmk
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# Via formats
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coreMaps := $(wildcard *-VegBIEN.*.csv)
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filenameVia = $(shell echo '$(1)'|grep --only-matching --extended-regexp\
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'^[a-zA-Z]+')
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# can't use --ignore-case because in Mac grep, a bug causes it to break [] exprs
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vias := $(strip $(sort $(foreach coreMap,$(coreMaps),$(call filenameVia,$(coreMap)))))
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1272
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aaronmk
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# Commands
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review_ = $(bin)/review <$(1) >for_review/$(1)
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review = $(call review_,$@)
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924
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aaronmk
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1272
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aaronmk
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join = env header_num=1 $(bin)/join_union_sort
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aaronmk
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selfMap_ = $(bin)/cols 0 0
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aaronmk
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# uniq: remove duplicates resulting from multiple outputs for the same input
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mkSelfMap = $(selfMap_) <$<|$(bin)/sort_map|uniq >$@
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744
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aaronmk
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aaronmk
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define chRoot
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$(bin)/ch_root <$< >$@
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$(review)
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endef
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785
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aaronmk
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##### General targets
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all: _always $(inputCoreMaps) dwc_maps vegx_maps self_maps ;
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aaronmk
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aaronmk
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.SUFFIXES: # turn off built-in suffix rules
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.SECONDARY: # don't automatically delete intermediate files
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aaronmk
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.DELETE_ON_ERROR: # delete target if recipe fails
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_always:
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.PHONY: _always
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188
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aaronmk
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383
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aaronmk
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clean: _always
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196
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aaronmk
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$(RM) $(all)
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188
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aaronmk
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924
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aaronmk
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all :=
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785
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aaronmk
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##### Core maps cleanup
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198
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aaronmk
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895
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aaronmk
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ifneq ($(filter .%.last_cleanup,$(MAKECMDGOALS)),)
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.%.last_cleanup: %
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$(bin)/in_place $< $(bin)/simplify_xpath
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$(bin)/in_place $< $(bin)/sort_map
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aaronmk
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touch $@
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aaronmk
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$(call review_,$<)
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895
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aaronmk
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else
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aaronmk
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$(inputCoreMaps): _always
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895
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aaronmk
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$(MAKE) $(@:%=.%.last_cleanup)
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endif
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350
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aaronmk
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1824
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aaronmk
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##### Self maps
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selfMaps :=
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viaCoreMap = $(via)-VegBIEN.%.csv
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viaSelfMap = $(via).self.%.csv
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viaCoreMaps = $(wildcard $(subst %,*,$(viaCoreMap)))
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define selfMapTargets
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selfMaps += $(viaCoreMaps:$(viaCoreMap)=$(viaSelfMap))
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$(viaSelfMap): $(viaCoreMap)
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$$(mkSelfMap)
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endef
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$(foreach via,$(vias),$(eval $(selfMapTargets)))
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ifneq ($(filter self_maps,$(MAKECMDGOALS)),)
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self_maps: _always $(selfMaps) ;
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else
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self_maps: _always
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$(MAKE) self_maps
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# re-run make so that cache of existing files for $(viaCoreMaps) is reset
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endif
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all += $(selfMaps)
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1272
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aaronmk
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##### DwC
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1115
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aaronmk
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1812
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aaronmk
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dwcMaps :=
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1115
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aaronmk
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1452
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aaronmk
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DwC.cs-VegBIEN.specimens.csv: DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv
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$(join) <$+ >$@
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1812
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aaronmk
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dwcMaps += DwC.cs-VegBIEN.specimens.csv
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1452
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aaronmk
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1802
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aaronmk
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DwC-VegBIEN.specimens.csv: DwC.cs-VegBIEN.specimens.csv
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1457
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aaronmk
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$(bin)/ci_map $< >$@
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1812
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aaronmk
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dwcMaps += DwC-VegBIEN.specimens.csv
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1118
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aaronmk
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1824
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dwc_maps: _always $(dwcMaps) ;
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1140
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aaronmk
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1812
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aaronmk
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all += $(dwcMaps)
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1115
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aaronmk
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1272
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aaronmk
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##### VegX
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212
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aaronmk
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1812
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aaronmk
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vegxMaps :=
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924
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aaronmk
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1818
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aaronmk
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rootAttrs := :[@xmlns:tcs="http://www.tdwg.org/schemas/tcs/1.01"]
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1816
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aaronmk
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1843
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aaronmk
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VegX-VegBIEN.organisms.csv: VegX-VegBIEN.stems.csv
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env \
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left_in_root='$(rootAttrs)/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation' \
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left_out_root='$(rootAttrs)/*s/individualOrganismObservation' \
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right_in_root='/stemobservation/*_id/plantobservation' \
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right_out_root='/plantobservation' \
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$(chRoot)
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vegxMaps += VegX-VegBIEN.organisms.csv
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438
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aaronmk
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VegX-VegBIEN.plots.csv: VegX-VegBIEN.organisms.csv
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188
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aaronmk
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env \
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aaronmk
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left_in_root='$(rootAttrs)/*s/individualOrganismObservation/*ID->/*s/plotObservation' \
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439
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aaronmk
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left_out_root='/*s/plotObservation' \
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right_in_root='/plantobservation/*_id/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent' \
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aaronmk
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right_out_root='/locationevent' \
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439
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aaronmk
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$(chRoot)
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1812
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aaronmk
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vegxMaps += VegX-VegBIEN.plots.csv
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439
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aaronmk
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vegx_maps: _always $(vegxMaps) ;
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aaronmk
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aaronmk
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all += $(vegxMaps)
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