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|
Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 22 Jun 2016 16:27:46 +0200
Description: Add autoconf stuff to enable simple library creation
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,16 @@
+lib_LTLIBRARIES = libsmithwaterman.la
+
+libsmithwatermandir=$(includedir)/smithwaterman
+libsmithwaterman_HEADERS=BandedSmithWaterman.h IndelAllele.h LeftAlign.h Mosaik.h Repeats.h SmithWatermanGotoh.h convert.h
+libsmithwaterman_la_SOURCES = BandedSmithWaterman.cpp IndelAllele.cpp LeftAlign.cpp Repeats.cpp SmithWatermanGotoh.cpp
+libsmithwaterman_la_LDFLAGS = -version-info @LIB_VERSION@
+
+libsmithwaterman_la_CPPFLAGS = $(INCLUDES)
+
+bin_PROGRAMS = smithwaterman
+smithwaterman_SOURCES = smithwaterman.cpp
+smithwaterman_LDADD = libsmithwaterman.la -ldisorder
+
+pkgconfigdir=$(libdir)/pkgconfig
+pkgconfig_DATA = libsmithwaterman.pc
+
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,61 @@
+# -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_INIT(smithwaterman, 0.0, erik.garrison@bc.edu)
+AC_CONFIG_HEADERS([config.h])
+
+AC_PREREQ(2.57)
+
+# Directory that contains install-sh and other auxiliary files
+AC_CONFIG_AUX_DIR([config])
+
+################################################################################
+# According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)
+# this macro should be after AC_INIT but before AM_INIT_AUTOMAKE
+################################################################################
+AC_CONFIG_MACRO_DIR(config)
+
+AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
+
+LIB_VERSION=0:0
+
+AC_SUBST([VERSION])
+AC_SUBST([LIB_VERSION])
+
+AC_SUBST([VERSION])
+
+# Checks for programs.
+AC_PROG_LN_S
+AC_PROG_INSTALL
+AC_PROG_LIBTOOL
+
+################################################################################
+# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
+# the AX_CXXFLAGS macro below.
+# So we cache the argument to configure
+# here in ARG_CXX_FLAGS (so that our macro does not override them)
+################################################################################
+ARG_CXX_FLAGS="$CXXFLAGS"
+AC_PROG_CXX
+
+#Ranlib handled by check for libtool
+CXXFLAGS="$ARG_CXX_FLAGS"
+AX_CXXFLAGS
+
+AC_SUBST(CXXFLAGS)
+
+CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"
+# Checks for libraries.
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([stdlib.h])
+
+AC_PROG_MAKE_SET
+
+AC_CONFIG_FILES([
+ Makefile
+ libsmithwaterman.pc
+ ])
+AC_OUTPUT
+
--- a/Makefile
+++ /dev/null
@@ -1,66 +0,0 @@
-# =========================================
-# MOSAIK Banded Smith-Waterman Makefile
-# (c) 2009 Michael Stromberg & Wan-Ping Lee
-# =========================================
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= smithwaterman.cpp BandedSmithWaterman.cpp SmithWatermanGotoh.cpp Repeats.cpp LeftAlign.cpp IndelAllele.cpp
-OBJECTS= $(SOURCES:.cpp=.o) disorder.o
-OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
-
-# ----------------
-# compiler options
-# ----------------
-
-# Use ?= to allow overriding from the env or command-line
-CXX?= c++
-CXXFLAGS?= -O3
-OBJ?= sw.o
-
-# I don't think := is useful here, since there is nothing to expand
-LDFLAGS:= -Wl,-s
-#CXXFLAGS=-g
-EXE:= smithwaterman
-LIBS=
-
-all: $(EXE) $(OBJ)
-
-.PHONY: all
-
-libsw.a: smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o
- ar rs $@ smithwaterman.o SmithWatermanGotoh.o disorder.o BandedSmithWaterman.o LeftAlign.o Repeats.o IndelAllele.o
-
-sw.o: BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o
- ld -r $^ -o sw.o -L.
- #$(CXX) $(CFLAGS) -c -o smithwaterman.cpp $(OBJECTS_NO_MAIN) -I.
-
-### @$(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $^ -I.
-$(EXE): smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o
- $(CXX) $(CFLAGS) $^ -I. -o $@
-
-#smithwaterman: $(OBJECTS)
-# $(CXX) $(CXXFLAGS) -o $@ $< -I.
-
-smithwaterman.o: smithwaterman.cpp disorder.o
- $(CXX) $(CXXFLAGS) -c -o $@ smithwaterman.cpp -I.
-
-disorder.o: disorder.cpp disorder.h
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-BandedSmithWaterman.o: BandedSmithWaterman.cpp BandedSmithWaterman.h
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-SmithWatermanGotoh.o: SmithWatermanGotoh.cpp SmithWatermanGotoh.h disorder.o
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-Repeats.o: Repeats.cpp
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-LeftAlign.o: LeftAlign.cpp
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-IndelAllele.o: IndelAllele.cpp
- $(CXX) $(CXXFLAGS) -c -o $@ $< -I.
-
-.PHONY: clean
-
-clean:
- @echo "Cleaning up."
- @rm -f *.o $(PROGRAM) *~
--- /dev/null
+++ b/libsmithwaterman.pc.in
@@ -0,0 +1,11 @@
+prefix=@prefix@
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include/smithwaterman
+
+
+Name: libsmithwaterman
+Version: @VERSION@
+Description: smith-waterman-gotoh alignment algorithm
+Libs: -L${libdir} -lsmithwaterman -ldisorder
+Cflags: -I${includedir}
|
