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#
Makefile from rmap software
#
#
Copyright (C) 2008 Cold Spring Harbor Laboratory,
#
University of Southern California and
#
Andrew D. Smith
#
#
Authors: Andrew D. Smith
#
#
This program is free software: you can redistribute it and/or modify
#
it under the terms of the GNU General Public License as published by
#
the Free Software Foundation, either version 3 of the License, or
#
(at your option) any later version.
#
#
This program is distributed in the hope that it will be useful,
#
but WITHOUT ANY WARRANTY; without even the implied warranty of
#
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
GNU General Public License for more details.
#
#
You should have received a copy of the GNU General Public License
#
along with this program. If not, see <http://www.gnu.org/licenses/>.
#
ifndef
SRC_ROOT
SRC_ROOT
=../../
endif
PROGS
= bedoverlap mapsifter extractseq deadzones
\
binreads sigoverlap
CXX
= g++
CFLAGS
= -Wall -fPIC -fmessage-length=50 -std=c++11
OPTFLAGS
= -O2
DEBUGFLAGS
= -g
SMITHLAB_CPP
= ../smithlab_cpp/
TEST_DIR
=
$(
SRC_ROOT
)
/test
ifeq
"
$(
shell
uname)
" "Darwin"
CFLAGS
+= -arch x86_64
ifeq
"
$(
shell
if [ `sysctl -n kern.osrelease | cut -d . -f 1` -ge 13 ];\
then echo 'true'; fi)
" "true"
CFLAGS
+= -stdlib=libstdc++
endif
endif
ifdef
PARALLEL
ifeq "$(PARALLEL)" "1"
CFLAGS += -fopenmp
endif
endif
ifdef
DEBUG
CFLAGS
+=
$(
DEBUGFLAGS
)
endif
ifdef
OPT
CFLAGS
+=
$(
OPTFLAGS
)
endif
all
:
$(
PROGS
)
%
.o
:
%
.cpp
%
.hpp
$(
CXX
)
$(
CFLAGS
)
-c -o
$@
$<
$(
PROGS
)
:
\
$(
addprefix
$(
SMITHLAB_CPP
)
/, GenomicRegion.o smithlab_os.o \
chromosome_utils.o smithlab_utils.o OptionParser.o)
install
: all
@mkdir -p
$(
SRC_ROOT
)
/bin
@install -m 755
$(
PROGS
)
$(
SRC_ROOT
)
/bin
%
:
%
.cpp
$(
CXX
)
$(
CFLAGS
)
-o
$@
$^
-I
$(
SMITHLAB_CPP
)
$(
LIBS
)
test_
%
:
%
@
$(
TEST_DIR
)
/
$@
$(
TEST_DIR
)
test
:
$(
addprefix
test_,
$(
PROGS
)
)
clean
:
@-rm -f
$(
PROGS
)
*
.o
*
.so
*
.a
*
~
.PHONY
: clean
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