From d96b03a4b02ea0dec936df3c9eab6bb0d2deee57 Mon Sep 17 00:00:00 2001 From: ravel-lab Date: Fri, 6 Sep 2024 10:44:08 -0400 Subject: [PATCH] updated Makefiles to write to macosx and linux in bin --- src/linux/Makefile | 2 +- src/linux/Makefile.bu | 138 ++++++++++++++++++ src/macosx/Makefile_buildMC | 2 +- src/macosx/Makefile_buildMC.bu | 138 ++++++++++++++++++ src/macosx/Makefile_buildModelTree | 2 +- src/macosx/Makefile_buildModelTree.bu | 76 ++++++++++ src/macosx/Makefile_clError | 2 +- src/macosx/Makefile_clError.bu | 138 ++++++++++++++++++ src/macosx/Makefile_classify | 2 +- src/macosx/Makefile_classify.bu | 135 +++++++++++++++++ src/macosx/Makefile_cut_tree | 2 +- src/macosx/Makefile_cut_tree.bu | 103 +++++++++++++ src/macosx/Makefile_est_error_thlds | 2 +- src/macosx/Makefile_est_error_thlds.bu | 138 ++++++++++++++++++ src/macosx/Makefile_est_error_thlds_mthread | 2 +- .../Makefile_est_error_thlds_mthread.bu | 138 ++++++++++++++++++ src/macosx/Makefile_fp_fn_rates | 2 +- src/macosx/Makefile_fp_fn_rates.bu | 138 ++++++++++++++++++ src/macosx/Makefile_pp_embedding | 2 +- src/macosx/Makefile_pp_embedding.bu | 138 ++++++++++++++++++ src/macosx/Makefile_pp_ref_sib_wr_ref_models | 2 +- .../Makefile_pp_ref_sib_wr_ref_models.bu | 138 ++++++++++++++++++ src/macosx/Makefile_pp_wr_selected_models | 2 +- src/macosx/Makefile_pp_wr_selected_models.bu | 138 ++++++++++++++++++ src/macosx/Makefile_rk_stats | 2 +- src/macosx/Makefile_rk_stats.bu | 138 ++++++++++++++++++ src/macosx/Makefile_sp_model_seq_lpps | 2 +- src/macosx/Makefile_sp_model_seq_lpps.bu | 138 ++++++++++++++++++ src/macosx/Makefile_taxon_model_rseq_lpps | 2 +- src/macosx/Makefile_taxon_model_rseq_lpps.bu | 138 ++++++++++++++++++ src/macosx/Makefile_tree_stitcher | 2 +- src/macosx/Makefile_tree_stitcher.bu | 98 +++++++++++++ src/macosx/Makefile_vicut | 2 +- src/macosx/Makefile_vicut.bu | 98 +++++++++++++ 34 files changed, 2183 insertions(+), 17 deletions(-) create mode 100644 src/linux/Makefile.bu create mode 100644 src/macosx/Makefile_buildMC.bu create mode 100644 src/macosx/Makefile_buildModelTree.bu create mode 100644 src/macosx/Makefile_clError.bu create mode 100644 src/macosx/Makefile_classify.bu create mode 100644 src/macosx/Makefile_cut_tree.bu create mode 100644 src/macosx/Makefile_est_error_thlds.bu create mode 100644 src/macosx/Makefile_est_error_thlds_mthread.bu create mode 100644 src/macosx/Makefile_fp_fn_rates.bu create mode 100644 src/macosx/Makefile_pp_embedding.bu create mode 100644 src/macosx/Makefile_pp_ref_sib_wr_ref_models.bu create mode 100644 src/macosx/Makefile_pp_wr_selected_models.bu create mode 100644 src/macosx/Makefile_rk_stats.bu create mode 100644 src/macosx/Makefile_sp_model_seq_lpps.bu create mode 100644 src/macosx/Makefile_taxon_model_rseq_lpps.bu create mode 100644 src/macosx/Makefile_tree_stitcher.bu create mode 100644 src/macosx/Makefile_vicut.bu diff --git a/src/linux/Makefile b/src/linux/Makefile index 71280cd..eeeaf9e 100644 --- a/src/linux/Makefile +++ b/src/linux/Makefile @@ -56,7 +56,7 @@ MKDIR = mkdir -p create-build-dir := $(shell $(CHK_DIR_EXISTS) .build || $(MKDIR) .build) SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/linux BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/linux/Makefile.bu b/src/linux/Makefile.bu new file mode 100644 index 0000000..71280cd --- /dev/null +++ b/src/linux/Makefile.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building classify +############################################################################# + +# Copyright (C) 2016 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = gcc #gcc-4.0 +CXX = g++ #g++-4.0 +FLAGS = -g # -fopenmp # -O2 # -g -O2 +CFLAGS = $(FLAGS) -Wall -D__SIM_SSE3 -O2 -D_GNU_SOURCE -dynamic -msse3 -fomit-frame-pointer -funroll-loops # -D_USE_PTHREADS +CXXFLAGS = $(FLAGS) -Wall -D__SIM_SSE3 -O2 -D_GNU_SOURCE -dynamic -msse3 -fomit-frame-pointer -funroll-loops # -D_USE_PTHREADS +INCPATH = -Isrc +LINK = g++ +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +create-build-dir := $(shell $(CHK_DIR_EXISTS) .build || $(MKDIR) .build) + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) + +OBJECTS = $(BUILDDIR)/classify.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains2.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +classify: $(OBJECTS) + $(CXX) $(FLAGS) $(OBJECTS) -o $(BINDIR)/classify + +$(BUILDDIR)/classify.o: $(SRCDIR)/classify.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/classify.o $(SRCDIR)/classify.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains2.o: $(SRCDIR)/MarkovChains2.cc $(SRCDIR)/MarkovChains2.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains2.o $(SRCDIR)/MarkovChains2.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_buildMC b/src/macosx/Makefile_buildMC index d59388f..f874deb 100644 --- a/src/macosx/Makefile_buildMC +++ b/src/macosx/Makefile_buildMC @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_buildMC.bu b/src/macosx/Makefile_buildMC.bu new file mode 100644 index 0000000..d59388f --- /dev/null +++ b/src/macosx/Makefile_buildMC.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building classify +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/buildMC.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +buildMC: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildMC + +$(BUILDDIR)/buildMC.o: $(SRCDIR)/buildMC.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/buildMC.o $(SRCDIR)/buildMC.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_buildModelTree b/src/macosx/Makefile_buildModelTree index 0f226ba..16e6c83 100644 --- a/src/macosx/Makefile_buildModelTree +++ b/src/macosx/Makefile_buildModelTree @@ -31,7 +31,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_buildModelTree.bu b/src/macosx/Makefile_buildModelTree.bu new file mode 100644 index 0000000..0f226ba --- /dev/null +++ b/src/macosx/Makefile_buildModelTree.bu @@ -0,0 +1,76 @@ + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -I../src +LIBS = # -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/buildModelTree.o \ + $(BUILDDIR)/Newick.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/strings.o + +buildModelTree: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildModelTree + +$(BUILDDIR)/buildModelTree.o: buildModelTree.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -I$(SRCDIR) -o $(BUILDDIR)/buildModelTree.o buildModelTree.cc + +$(BUILDDIR)/Newick.o: Newick.hh Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o Newick.cc + +$(BUILDDIR)/IOCUtilities.o: IOCUtilities.h IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o IOCUtilities.c + +$(BUILDDIR)/IOCppUtilities.o: IOCppUtilities.cc IOCppUtilities.hh + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o IOCppUtilities.cc + +$(BUILDDIR)/CppUtilities.o: CppUtilities.cc CppUtilities.hh + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o CppUtilities.cc + +$(BUILDDIR)/CUtilities.o: CUtilities.c CUtilities.h + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o CUtilities.c + +$(BUILDDIR)/strings.o: strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o strings.cc + +clean: + rm -f $(BUILDDIR)/*.o + +clean-all: + rm -rf $(BUILDDIR) $(BINDIR)/readNewick diff --git a/src/macosx/Makefile_clError b/src/macosx/Makefile_clError index a54198e..1be3257 100644 --- a/src/macosx/Makefile_clError +++ b/src/macosx/Makefile_clError @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_clError.bu b/src/macosx/Makefile_clError.bu new file mode 100644 index 0000000..a54198e --- /dev/null +++ b/src/macosx/Makefile_clError.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building clError +############################################################################# + +# Copyright (C) 2016 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/clError.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +clError: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/clError + +$(BUILDDIR)/clError.o: $(SRCDIR)/clError.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/clError.o $(SRCDIR)/clError.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_classify b/src/macosx/Makefile_classify index e388496..5954e4c 100644 --- a/src/macosx/Makefile_classify +++ b/src/macosx/Makefile_classify @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_classify.bu b/src/macosx/Makefile_classify.bu new file mode 100644 index 0000000..e388496 --- /dev/null +++ b/src/macosx/Makefile_classify.bu @@ -0,0 +1,135 @@ + +############################################################################# +# Makefile for building classify +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -pthread -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/classify.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +classify: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/classify + +$(BUILDDIR)/classify.o: $(SRCDIR)/classify.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/classify.o $(SRCDIR)/classify.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_cut_tree b/src/macosx/Makefile_cut_tree index c56855f..9fb084d 100644 --- a/src/macosx/Makefile_cut_tree +++ b/src/macosx/Makefile_cut_tree @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_cut_tree.bu b/src/macosx/Makefile_cut_tree.bu new file mode 100644 index 0000000..c56855f --- /dev/null +++ b/src/macosx/Makefile_cut_tree.bu @@ -0,0 +1,103 @@ + +############################################################################# +# Makefile for cut_tree +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = #-Isrc +LIBS = # -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/cut_tree.o \ + $(BUILDDIR)/Newick.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/strings.o \ + +####### Build rules + +cut_tree: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/cut_tree + +$(BUILDDIR)/cut_tree.o: cut_tree.cc Newick.hh Newick.cc IOCUtilities.h IOCUtilities.c IOCppUtilities.cc + $(CXX) -c $(FLAGS) $(INCPATH) -I$(SRCDIR) -o $(BUILDDIR)/cut_tree.o cut_tree.cc + +$(BUILDDIR)/Newick.o: Newick.hh Newick.cc + $(CXX) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o Newick.cc + +$(BUILDDIR)/IOCUtilities.o: IOCUtilities.h IOCUtilities.c + $(CC) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o IOCUtilities.c + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + + +clean: + rm -f $(BUILDDIR)/*.o + +clean-all: + rm -rf $(BUILDDIR) $(BINDIR)/cut_tree diff --git a/src/macosx/Makefile_est_error_thlds b/src/macosx/Makefile_est_error_thlds index cadc719..0afce9d 100644 --- a/src/macosx/Makefile_est_error_thlds +++ b/src/macosx/Makefile_est_error_thlds @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_est_error_thlds.bu b/src/macosx/Makefile_est_error_thlds.bu new file mode 100644 index 0000000..cadc719 --- /dev/null +++ b/src/macosx/Makefile_est_error_thlds.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building est_error_thlds.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -std=c++1z -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/est_error_thlds.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +est_error_thlds: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/est_error_thlds + +$(BUILDDIR)/est_error_thlds.o: $(SRCDIR)/est_error_thlds.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/est_error_thlds.o $(SRCDIR)/est_error_thlds.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_est_error_thlds_mthread b/src/macosx/Makefile_est_error_thlds_mthread index d10e291..bd678b1 100644 --- a/src/macosx/Makefile_est_error_thlds_mthread +++ b/src/macosx/Makefile_est_error_thlds_mthread @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_est_error_thlds_mthread.bu b/src/macosx/Makefile_est_error_thlds_mthread.bu new file mode 100644 index 0000000..d10e291 --- /dev/null +++ b/src/macosx/Makefile_est_error_thlds_mthread.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building est_error_thlds.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/est_error_thlds_mthread.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +est_error_thlds_mthread: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/est_error_thlds_mthread + +$(BUILDDIR)/est_error_thlds_mthread.o: $(SRCDIR)/est_error_thlds_mthread.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/est_error_thlds_mthread.o $(SRCDIR)/est_error_thlds_mthread.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_fp_fn_rates b/src/macosx/Makefile_fp_fn_rates index e8a7db0..7c7746f 100644 --- a/src/macosx/Makefile_fp_fn_rates +++ b/src/macosx/Makefile_fp_fn_rates @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_fp_fn_rates.bu b/src/macosx/Makefile_fp_fn_rates.bu new file mode 100644 index 0000000..e8a7db0 --- /dev/null +++ b/src/macosx/Makefile_fp_fn_rates.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building fp_fn_rates.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/fp_fn_rates.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +fp_fn_rates: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/fp_fn_rates + +$(BUILDDIR)/fp_fn_rates.o: $(SRCDIR)/fp_fn_rates.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/fp_fn_rates.o $(SRCDIR)/fp_fn_rates.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_pp_embedding b/src/macosx/Makefile_pp_embedding index 993a54b..523a89d 100644 --- a/src/macosx/Makefile_pp_embedding +++ b/src/macosx/Makefile_pp_embedding @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_pp_embedding.bu b/src/macosx/Makefile_pp_embedding.bu new file mode 100644 index 0000000..993a54b --- /dev/null +++ b/src/macosx/Makefile_pp_embedding.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building pp_embedding.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/pp_embedding.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +pp_embedding: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/pp_embedding + +$(BUILDDIR)/pp_embedding.o: $(SRCDIR)/pp_embedding.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/pp_embedding.o $(SRCDIR)/pp_embedding.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_pp_ref_sib_wr_ref_models b/src/macosx/Makefile_pp_ref_sib_wr_ref_models index 8c1c619..76afb78 100644 --- a/src/macosx/Makefile_pp_ref_sib_wr_ref_models +++ b/src/macosx/Makefile_pp_ref_sib_wr_ref_models @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_pp_ref_sib_wr_ref_models.bu b/src/macosx/Makefile_pp_ref_sib_wr_ref_models.bu new file mode 100644 index 0000000..8c1c619 --- /dev/null +++ b/src/macosx/Makefile_pp_ref_sib_wr_ref_models.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building pp_ref_sib_wr_ref_models.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang # gcc #/opt/local/bin/gcc-mp-4.7 #gcc-4.0 +CXX = clang # g++ #/opt/local/bin/g++-mp-4.7 #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/pp_ref_sib_wr_ref_models.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +pp_ref_sib_wr_ref_models: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/pp_ref_sib_wr_ref_models + +$(BUILDDIR)/pp_ref_sib_wr_ref_models.o: $(SRCDIR)/pp_ref_sib_wr_ref_models.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/pp_ref_sib_wr_ref_models.o $(SRCDIR)/pp_ref_sib_wr_ref_models.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_pp_wr_selected_models b/src/macosx/Makefile_pp_wr_selected_models index 104c9a1..814c536 100644 --- a/src/macosx/Makefile_pp_wr_selected_models +++ b/src/macosx/Makefile_pp_wr_selected_models @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_pp_wr_selected_models.bu b/src/macosx/Makefile_pp_wr_selected_models.bu new file mode 100644 index 0000000..104c9a1 --- /dev/null +++ b/src/macosx/Makefile_pp_wr_selected_models.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building pp_wr_selected_models +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/pp_wr_selected_models.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +pp_wr_selected_models: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/pp_wr_selected_models + +$(BUILDDIR)/pp_wr_selected_models.o: $(SRCDIR)/pp_wr_selected_models.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/pp_wr_selected_models.o $(SRCDIR)/pp_wr_selected_models.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_rk_stats b/src/macosx/Makefile_rk_stats index cae8af2..e53f597 100644 --- a/src/macosx/Makefile_rk_stats +++ b/src/macosx/Makefile_rk_stats @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_rk_stats.bu b/src/macosx/Makefile_rk_stats.bu new file mode 100644 index 0000000..cae8af2 --- /dev/null +++ b/src/macosx/Makefile_rk_stats.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building rk_stats.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/rk_stats.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +rk_stats: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/rk_stats + +$(BUILDDIR)/rk_stats.o: $(SRCDIR)/rk_stats.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/rk_stats.o $(SRCDIR)/rk_stats.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_sp_model_seq_lpps b/src/macosx/Makefile_sp_model_seq_lpps index 1c70d99..d484250 100644 --- a/src/macosx/Makefile_sp_model_seq_lpps +++ b/src/macosx/Makefile_sp_model_seq_lpps @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_sp_model_seq_lpps.bu b/src/macosx/Makefile_sp_model_seq_lpps.bu new file mode 100644 index 0000000..1c70d99 --- /dev/null +++ b/src/macosx/Makefile_sp_model_seq_lpps.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building est_error_thlds.cc +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -D__SIM_SSE3 # -Wall -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -msse3 -O2 # -D_GNU_SOURCE -g -O2 -D__SIM_SSE3 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = -std=c++1z $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/sp_model_seq_lpps.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +sp_model_seq_lpps: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/sp_model_seq_lpps + +$(BUILDDIR)/sp_model_seq_lpps.o: $(SRCDIR)/sp_model_seq_lpps.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/sp_model_seq_lpps.o $(SRCDIR)/sp_model_seq_lpps.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_taxon_model_rseq_lpps b/src/macosx/Makefile_taxon_model_rseq_lpps index 8e302f7..af8325b 100644 --- a/src/macosx/Makefile_taxon_model_rseq_lpps +++ b/src/macosx/Makefile_taxon_model_rseq_lpps @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_taxon_model_rseq_lpps.bu b/src/macosx/Makefile_taxon_model_rseq_lpps.bu new file mode 100644 index 0000000..8e302f7 --- /dev/null +++ b/src/macosx/Makefile_taxon_model_rseq_lpps.bu @@ -0,0 +1,138 @@ + +############################################################################# +# Makefile for building taxon_model_rseq_lpps +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -D__SIM_SSE3 # -Wall -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -msse3 -O2 # -D_GNU_SOURCE -g -O2 -D__SIM_SSE3 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = -std=c++1z $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/taxon_model_rseq_lpps.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/MarkovChains.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CStatUtilities.o \ + $(BUILDDIR)/CppStatUtilities.o \ + $(BUILDDIR)/StatUtilities.o \ + $(BUILDDIR)/DNAsequence.o \ + $(BUILDDIR)/Newick.o \ + +####### Build rules + +taxon_model_rseq_lpps: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/taxon_model_rseq_lpps + +$(BUILDDIR)/taxon_model_rseq_lpps.o: $(SRCDIR)/taxon_model_rseq_lpps.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/taxon_model_rseq_lpps.o $(SRCDIR)/taxon_model_rseq_lpps.cc + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c + +$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc + +$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc + +$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c + +$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc + +$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc + +$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c + $(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c + +$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + + +$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ + $(SRCDIR)/CUtilities.h \ + $(SRCDIR)/CUtilities.c \ + $(SRCDIR)/CppUtilities.hh \ + $(SRCDIR)/CppUtilities.cc \ + $(SRCDIR)/strings.hh \ + $(SRCDIR)/strings.cc \ + $(SRCDIR)/DNAsequence.hh \ + $(SRCDIR)/DNAsequence.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc + + + +clean: + -$(DEL_FILE) $(OBJECTS) + -$(DEL_FILE) *~ core *.core + + + + +distclean: clean + -$(DEL_FILE) $(TARGET) + -$(DEL_FILE) Makefile diff --git a/src/macosx/Makefile_tree_stitcher b/src/macosx/Makefile_tree_stitcher index 2bbb8f5..b3bc1c2 100644 --- a/src/macosx/Makefile_tree_stitcher +++ b/src/macosx/Makefile_tree_stitcher @@ -53,7 +53,7 @@ CHK_DIR_EXISTS= test -d MKDIR = mkdir -p SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_tree_stitcher.bu b/src/macosx/Makefile_tree_stitcher.bu new file mode 100644 index 0000000..2bbb8f5 --- /dev/null +++ b/src/macosx/Makefile_tree_stitcher.bu @@ -0,0 +1,98 @@ + +############################################################################# +# Makefile for tree_stitcher +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = $(FLAGS) +INCPATH = -I../src +LIBS = # -lm # -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/tree_stitcher.o \ + $(BUILDDIR)/Newick.o \ + $(BUILDDIR)/IOCUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/CUtilities.o \ + $(BUILDDIR)/strings.o + +tree_stitcher: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/tree_stitcher + +$(BUILDDIR)/tree_stitcher.o: tree_stitcher.cc + $(CXX) -c $(FLAGS) $(INCPATH) -I$(SRCDIR) -o $(BUILDDIR)/tree_stitcher.o tree_stitcher.cc + +$(BUILDDIR)/Newick.o: Newick.hh Newick.cc + $(CXX) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o Newick.cc + +$(BUILDDIR)/IOCUtilities.o: IOCUtilities.h IOCUtilities.c + $(CC) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o IOCUtilities.c + +$(BUILDDIR)/IOCppUtilities.o: IOCppUtilities.cc IOCppUtilities.hh + $(CXX) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o IOCppUtilities.cc + +$(BUILDDIR)/CppUtilities.o: CppUtilities.cc CppUtilities.hh + $(CXX) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o CppUtilities.cc + +$(BUILDDIR)/CUtilities.o: CUtilities.c CUtilities.h + $(CC) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o CUtilities.c + +$(BUILDDIR)/strings.o: strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o strings.cc + +clean: + rm -f $(BUILDDIR)/*.o + +clean-all: + rm -rf $(BUILDDIR) $(BINDIR)/readNewick diff --git a/src/macosx/Makefile_vicut b/src/macosx/Makefile_vicut index a964d7a..05f077b 100644 --- a/src/macosx/Makefile_vicut +++ b/src/macosx/Makefile_vicut @@ -55,7 +55,7 @@ MKDIR = mkdir -p ####### Files SRCDIR = . -BINDIR = ../bin +BINDIR = ../../bin/macosx BUILDDIR= .build create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) diff --git a/src/macosx/Makefile_vicut.bu b/src/macosx/Makefile_vicut.bu new file mode 100644 index 0000000..a964d7a --- /dev/null +++ b/src/macosx/Makefile_vicut.bu @@ -0,0 +1,98 @@ + +############################################################################# +# Makefile for building vicut +############################################################################# + +# Copyright (C) 2017 Pawel Gajer pgajer@gmail.com and Jacques Ravel jravel@som.umaryland.edu + +# Permission to use, copy, modify, and distribute this software and its +# documentation with or without modifications and for any purpose and +# without fee is hereby granted, provided that any copyright notices +# appear in all copies and that both those copyright notices and this +# permission notice appear in supporting documentation, and that the +# names of the contributors or copyright holders not be used in +# advertising or publicity pertaining to distribution of the software +# without specific prior permission. + +# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +# OR PERFORMANCE OF THIS SOFTWARE. + +####### Compiler, tools and options + +CC = clang #gcc #gcc-4.0 +CXX = clang #g++ #g++-4.0 +LINK = clang #g++ +LDFLAGS = -std=c++11 -lc++abi -lstdc++ +FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter +CFLAGS = $(FLAGS) +CXXFLAGS = -std=c++11 $(FLAGS) +INCPATH = -Isrc +LIBS = -lm # -pthread -L../../lib -lkmerstats +AR = ar cq +RANLIB = ranlib -s +TAR = tar -cf +COMPRESS = gzip -9f +COPY = cp -f +SED = sed +COPY_FILE = cp -f +COPY_DIR = cp -f -R +INSTALL_FILE = $(COPY_FILE) +INSTALL_DIR = $(COPY_DIR) +INSTALL_PROGRAM = $(COPY_FILE) +DEL_FILE = rm -f +SYMLINK = ln -sf +DEL_DIR = rmdir +MOVE = mv -f +CHK_DIR_EXISTS= test -d +MKDIR = mkdir -p + +####### Files + +SRCDIR = . +BINDIR = ../bin +BUILDDIR= .build + +create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) +create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) + +OBJECTS = $(BUILDDIR)/vicut.o \ + $(BUILDDIR)/IOUtilities.o \ + $(BUILDDIR)/IOCppUtilities.o \ + $(BUILDDIR)/Newick.o \ + $(BUILDDIR)/strings.o \ + $(BUILDDIR)/CppUtilities.o \ + $(BUILDDIR)/CUtilities.o + + +vicut: $(OBJECTS) + $(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/vicut + +$(BUILDDIR)/vicut.o: vicut.cc $(SRCDIR)/IOUtilities.c $(SRCDIR)/IOCppUtilities.cc + $(CXX) -c $(CXXFLAGS) -I$(SRCDIR) $(INCPATH) -o $(BUILDDIR)/vicut.o vicut.cc + +$(BUILDDIR)/IOUtilities.o: $(SRCDIR)/IOUtilities.c + $(CC) -c $(FLAGS) -o $(BUILDDIR)/IOUtilities.o $(SRCDIR)/IOUtilities.c + +$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc $(SRCDIR)/IOUtilities.c + $(CXX) -c $(FLAGS) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc + +$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.cc + $(CXX) -c $(FLAGS) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc + +$(BUILDDIR)/CppUtilities.o: CppUtilities.cc CppUtilities.hh + $(CXX) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o CppUtilities.cc + +$(BUILDDIR)/CUtilities.o: CUtilities.c CUtilities.h + $(CC) -c $(FLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o CUtilities.c + +$(BUILDDIR)/strings.o: strings.cc + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o strings.cc + +clean: + rm -f $(BUILDDIR)/*.o