SHELL | shell used for executing system commands. | /bin/sh
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CXX | c++ compiler. | set by OS.
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CFLAGS | compiler flags. | -Wall -ggdb -O2 -pthread
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PACKAGENAME | the name of the executable file. | cold
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VERSION | the version of the program. | 1.0.0
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forceremakeconfig | indicates whether configuration file needs to be remade.
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forceremakevar | indicates whether .variable file needs to be remade.
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mainsearchdir | directory in which application files are based. | $(HOME)/$(PACKAGENAME)
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prefix | directory in which installed files should be stored. | /usr/local/
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exec_prefix | directory in which executable files should be stored. | $(prefix)
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bindir | directory in which the actual binary executable files should be stored.
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DESTDIR | user input prefix to installation directory.
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installbin | executable files to be installed. | $(PACKAGENAME) DNAml Utilities/setup Utilities/reordermatrix Utilities/summats
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installdat | data files to be installed. | .variables .flags Models/parametermatrices Models/ECMq.txt Data/testtrees Data/testdata Models/mixture Models/models Models/masks Models/standardmodelmatrices Utilities/codonlistexample.txt Utilities/coldcodonorder.txt
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installdoc | documentation files to be installed. | Documentation/cold.info Documentation/files.info Documentation/installation.info Documentation/utilities.info
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INSTALL | command for installing programs. | set by OS.
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