makefile

一个神经网络工具箱

#
# Generic Linux/Unix Makefile for PHYLIP 3.6.
#
# You should not need to change anything, though if you want you could
# change the first (noncomment) statement to some directory location
# that might be more useful.
# The compressed tar archive phylip.tar.Z when uncompressed and extracted
# puts the source code into a directory ./src, and also makes two other
# directories ./exe and ./doc for the final executables and the documentation
# files.  Only change the EXEDIR settings if you want something different
# from that structure.
# If it causes trouble in compiling, the CFLAGS statement below may also need
# to be changed.
#
#  To use the PHYLIP v3.6 Makefile, type
#      make install       to compile the whole package and install
#                           the executables in $(EXEDIR), and then
#                           remove the object files to save space
#      make all           to compile the whole package but not install it
#                           or remove the object files
#      make put           to move the executables into $(EXEDIR)
#      make clean         to remove all object files and executables from the
#                           current directory
#      make dnaml         to compile and link one program, (in this example,
#                           DnaML) and leave the executable and object files
#                           in the current directory (where the source code is).
#                           You will have to move the executable in to the
#                           executables directory (e.g. "mv dnaml ../exe")
#                           Note that the program name should be lower case.
# 
# ----------------------------------------------------------------------------
#  (Starting here is the section where you may want to change things)
# ----------------------------------------------------------------------------
#
# these are the statements we have been talking about:
# one of the reasons for changing them would be to put the executables
# on a different file system.
# The default configuration is to have within the overall PHYLIP
# directory three subdirectories:  "src" for source code, "exe" for the
# executables, and "doc" for the documentation files.
#
# the following specifies the directory where the executables will be placed
EXEDIR  = ../exe
#
# ----------------------------------------------------------------------------
#
# In the following statements (the ones that set CFLAGS, DFLAGS, LIBS
# and DLIBS, CC and DC) you should make sure each is set properly.
# Usually this will simply involve making sure that the proper statement
# has no "#" as its first character and that all other possibilities
# have "#" for their first character.
#
# ----------------------------------------------------------------------------
#
# This is the CFLAGS statement:
#
# if these statements say "-g"  and that causes trouble, remove the "-g"
# if the "-lX11" does not work (X compiling not working), you may want to
# remove that switch or fix it.
#
# Here are some possible CFLAGS statements:
#
#
#A minimal one
CFLAGS =
#
# A basic one for debugging
#CFLAGS  = -g 
#
# An optimized one for gcc
#CFLAGS  = -O3 -fomit-frame-pointer
#
# For some serious debugging using Gnu gcc
#
#CFLAGS=-g -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes  -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
#
# For Digital Alpha systems with Compaq Tru64 Unix
# (however, be aware that this may cause floating-point problems in programs
#  like Dnaml owing to not using IEEE floating point standards).
#CFLAGS = -fast
#
# ----------------------------------------------------------------------------
#
# and here are some possible DFLAGS statements:
#
# A minimal one
#DFLAGS  = -DX $(CFLAGS)
#
# A basic one for debugging
#DFLAGS  = -g -DX
#
#
# For Gnu C++ for runs
#DFLAGS  = -I/usr/X11R6/include -O3 -DX -fomit-frame-pointer
#
# For Digital Alpha systems with Compaq Tru64 Unix
#DFLAGS = -DX -fast 
#
# for Linux with X Windows development packages installed
# or for MacOS X with X Windows installed
DFLAGS = $(CFLAGS) -DX -I/usr/X11R6/include
#
# ----------------------------------------------------------------------------
#
# These are the libraries for the CC and DC compiles, respectively
#
LIBS    = -lm
#
# if the Xlib library for the X windowing system is somewhere
# unexpected, you may have to change the path /usr/X11R6/lib in this one
#
# For gcc for Linux with X windows development packages installed
# or for MacOS X with X windows installed
DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lXt
#
# ----------------------------------------------------------------------------
#
# The next two assignments are the invocations of the compiler for the
# ordinary compiles and the tree-drawing programs, CC and DC
#
# This one specifies the "cc" C compiler
CC        = cc $(CFLAGS)
#
#  To use GCC instead, if it is not the compiler that "cc" invokes
#CC        = gcc $(CFLAGS)
#
# This one specifies the "cc" C compiler for the Draw programs
DC        = cc $(DFLAGS)
#
# To use GCC instead, if it is not the compiler that "cc" invokes
#DC        = gcc $(DFLAGS)
#
# ----------------------------------------------------------------------------
#  (After this point there should not be any reason to change anything)
# ----------------------------------------------------------------------------
#
#
# the list of programs
#
PROGS   =          clique consense contml contrast dnacomp dnadist \
                   dnainvar dnaml dnamlk dnamove dnapars dnapenny \
                   dolmove dollop dolpenny factor fitch gendist kitsch \
                   mix move neighbor pars penny proml promlk protdist \
                   protpars restdist restml retree seqboot treedist \
                   drawgram drawtree
#
# general commands
#

#
#  The first uses a symbol you are unlikely to type.  It is the one that
#  is executed if you just type "make".  It tells you how to use the
#  Makefile.
#
a1b2c3d4:
	@echo ""
	@echo " To use the PHYLIP v3.6 Makefile, type"
	@echo "     make install       to compile the whole package and install"
	@echo "                          the executables in $(EXEDIR), and then"
	@echo "                          remove the object files to save space"
	@echo "     make all           to compile the whole package but not install it"
	@echo "                          or remove the object files"
	@echo "     make put           to move the executables into $(EXEDIR)"
	@echo "     make clean         to remove all object files and executables from the"
	@echo "                          current directory"
	@echo "     make dnaml         to compile and link one program, (in this example,"
	@echo "                          DnaML) and leave the executable and object files"
	@echo "                          in the current directory (where the source code is)."
	@echo "                          You will have to move the executable into the"
	@echo "                          executables directory (e.g. "mv dnaml $(EXEDIR)")"
	@echo "                          Note that the program name should be lower case."
	@echo " "

introduce:
	@echo "Building PHYLIP version 3.6"

all:        introduce $(PROGS)
	@echo "Finished compiling."
	@echo ""

install:        all put clean
	@echo "Done."
	@echo ""

put:
	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
	@mkdir -p $(EXEDIR)
	@cp $(PROGS) $(EXEDIR)
	@echo "Installing font files in $(EXEDIR)"
	@cp font* $(EXEDIR)
	@echo "Finished installation."
	@echo ""

clean:
	@echo "Removing object files to save space"
	@rm -f *.o
	@echo "Finished removing object files.  Now will remove"
	@echo "executable files from the current directory, but not from the"
	@echo "executables directory.  (If some are not here, the makefile"
	@echo "will terminate with an error message but this is not a problem)"
	@echo ""
	@echo "Removing executables from this directory"
	@rm -f $(PROGS)
	@echo "Finished cleanup."
	@echo ""

#
# compile the shared stuff
#

phylip.o:     phylip.c phylip.h
	$(CC) -c phylip.c

seq.o:        seq.c phylip.h seq.h
	$(CC) -c seq.c

disc.o:   disc.c phylip.h disc.h
	$(CC) -c disc.c

discrete.o:        discrete.c discrete.h phylip.h
	$(CC) -c discrete.c

dollo.o:        dollo.c phylip.h dollo.h
	$(CC) -c dollo.c

wagner.o:        wagner.c phylip.h wagner.h
	$(CC) -c wagner.c

dist.o:   dist.c phylip.h dist.h
	$(CC) -c dist.c