Alternative build system

Makefile.simple

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+############################################################################
+#
+# Simple, portable Makefile for POSIX platforms.
+# 
+# Author: J. Bacon
+#
+# This Makefile and it's children provide a simple and portable way to
+# build NGS on POSIX platforms.  It was originally tested with BSD and GNU
+# make on CentOS Linux, FreeBSD, Mac OS X, and NetBSD.
+#
+# The associated build.simple script can be used to invoke make more
+# easily and provide flags for not-quite-standard systems such as OS X.
+#
+# LICENSE: Public Domain
+#
+# Variables that are conditionally assigned (with ?=) can be overridden
+# via the command line as follows:
+#
+#       make VAR=value
+#
+# For example, MacPorts installs to /opt/local instead of the default
+# /usr/local, and hence might use the following:
+# 
+#       make PREFIX=/opt/local
+#
+# Different systems may also use different compilers and keep libraries in
+# different locations:
+#
+#       make CC=gcc CFLAGS=-O2 LDFLAGS="-L/usr/X11R6 -lX11"
+#
+# Variables can also inheret values from parent Makefiles (as in *BSD ports).
+#
+# Lastly, they can be overridden by the environment, e.g.
+# 
+#       setenv CFLAGS "-O -Wall -pipe"
+#       make
+#
+# All these override methods allow the Makefile to respect the environment
+# in which it is used.
+#
+# You can append values to variables within this Makefile (with +=).
+# However, this should not be used to add compiler-specific flags like
+# -Wall, as this would disrespect the environment.
+############################################################################
+
+MAKE    ?= make
+DIRS    = ngs-sdk ngs-java
+
+MKDIR   ?= mkdir
+INSTALL ?= install
+RM      ?= rm
+
+PREFIX  ?= /usr/local
+DESTDIR ?= ./stage
+
+# Defaults for most Unix.  Override for OS X dylibs.
+# Some make implementations do not pass local make variables to child processes
+# by default, so pass SO_NAME, etc. manually for portability.
+SO_EXT          ?= so
+SO_MAJ          = 1
+SO_MIN          = 3
+SO_REV          = 0
+SO_VER          = ${SO_MAJ}.${SO_MIN}.${SO_REV}
+SO_NAME         ?= libngs-sdk.${SO_EXT}.${SO_VER}
+SO_SHORT_NAME   ?= libngs-sdk.${SO_EXT}.${SO_MAJ}
+SO_FLAGS        ?= -Wl,-soname=libngs-sdk.${SO_EXT}.${SO_MAJ}
+
+all:
+	@for dir in ${DIRS}; do \
+	    ${MAKE} -C $$dir -f Makefile.simple \
+		SO_NAME=${SO_NAME} SO_SHORT_NAME=${SO_SHORT_NAME} \
+		SO_FLAGS=${SO_FLAGS} SO_EXT=${SO_EXT}; \
+	done
+
+clean:
+	@for dir in ${DIRS}; do \
+	    ${MAKE} -C $$dir -f Makefile.simple clean; \
+	done
+	${RM} -rf ${DESTDIR}
+
+install: all
+	${MKDIR} -p ${DESTDIR}${PREFIX}/lib
+	${INSTALL} -c ngs-sdk/*/*.a ngs-sdk/language/*/*.a \
+		${DESTDIR}${PREFIX}/lib
+	${INSTALL} -c ngs-sdk/*.${SO_EXT}* ${DESTDIR}${PREFIX}/lib
+	${MKDIR} -p ${DESTDIR}${PREFIX}/include/ngs/adapter \
+		${DESTDIR}${PREFIX}/include/ngs/inl \
+		${DESTDIR}${PREFIX}/include/ngs/itf \
+		${DESTDIR}${PREFIX}/include/ngs/unix/`uname -p`
+	${INSTALL} -c ngs-sdk/ngs/*.hpp ${DESTDIR}${PREFIX}/include/ngs
+	${INSTALL} -c ngs-sdk/ngs/adapter/*.hpp ngs-sdk/ngs/adapter/*.h \
+		${DESTDIR}${PREFIX}/include/ngs/adapter
+	${INSTALL} -c ngs-sdk/ngs/inl/*.hpp ${DESTDIR}${PREFIX}/include/ngs/inl
+	${INSTALL} -c ngs-sdk/ngs/itf/*.hpp ngs-sdk/ngs/itf/*.h \
+		${DESTDIR}${PREFIX}/include/ngs/itf
+	${INSTALL} -c ngs-sdk/ngs/unix/`uname -p`/*.h \
+		${DESTDIR}${PREFIX}/include/ngs/unix/`uname -p`
+	${MKDIR} -p ${DESTDIR}${PREFIX}/share/java/classes
+	${INSTALL} -c ngs-java/ngs-java.jar \
+		${DESTDIR}${PREFIX}/share/java/classes

build.simple

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+#!/bin/sh -e
+
+# Note:
+# This script is only for recording platform-specific flags.
+# Makefile.simple should not depend on this script.
+# You can simple run
+#
+#   make -f Makefile.simple CXX=...
+
+# Default case below works for FreeBSD, Linux, and Mac.
+# If another platform requires special compiler flags, add a case.
+
+case `uname` in
+Darwin)
+    # FIXME: Not sure about the best SO_FLAGS
+    export CXXFLAGS='-g -O -fPIC'
+    export SO_EXT=dylib
+    export SO_FLAGS=''
+    ;;
+*)
+    export CXXFLAGS='-g -O -fPIC'
+    ;;
+esac
+
+make -f Makefile.simple $@

ngs-java/Makefile.simple

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+
+BIN     = ngs-java.jar
+
+RM	?= rm
+
+all:	${BIN}
+
+${BIN}:	ngs/*.java
+	javac \
+		ngs/ErrorMsg.java \
+		ngs/Statistics.java \
+		ngs/Fragment.java \
+		ngs/FragmentIterator.java \
+		ngs/Read.java \
+		ngs/ReadIterator.java \
+		ngs/ReadGroup.java \
+		ngs/ReadGroupIterator.java \
+		ngs/Alignment.java \
+		ngs/AlignmentIterator.java \
+		ngs/PileupEvent.java \
+		ngs/PileupEventIterator.java \
+		ngs/Pileup.java \
+		ngs/PileupIterator.java \
+		ngs/Reference.java \
+		ngs/ReferenceIterator.java \
+		ngs/ReadCollection.java \
+		ngs/Package.java \
+		-d . -classpath . -sourcepath .:itf:
+	javac  \
+		ngs/itf/Refcount.java \
+		ngs/itf/StatisticsItf.java \
+		ngs/itf/FragmentItf.java \
+		ngs/itf/FragmentIteratorItf.java \
+		ngs/itf/ReadItf.java \
+		ngs/itf/ReadIteratorItf.java \
+		ngs/itf/ReadGroupItf.java \
+		ngs/itf/ReadGroupIteratorItf.java \
+		ngs/itf/AlignmentItf.java \
+		ngs/itf/AlignmentIteratorItf.java \
+		ngs/itf/PileupEventItf.java \
+		ngs/itf/PileupEventIteratorItf.java \
+		ngs/itf/PileupItf.java \
+		ngs/itf/PileupIteratorItf.java \
+		ngs/itf/ReferenceItf.java \
+		ngs/itf/ReferenceIteratorItf.java \
+		ngs/itf/ReadCollectionItf.java \
+		-d . -classpath . -sourcepath .:itf:
+	javac \
+		gov/nih/nlm/ncbi/ngs/DownloadManager.java \
+		gov/nih/nlm/ncbi/ngs/FileCreator.java \
+		gov/nih/nlm/ncbi/ngs/HttpManager.java \
+		gov/nih/nlm/ncbi/ngs/LibDependencies.java \
+		gov/nih/nlm/ncbi/ngs/LibManager.java \
+		gov/nih/nlm/ncbi/ngs/LibPathIterator.java \
+		gov/nih/nlm/ncbi/ngs/LibVersionChecker.java \
+		gov/nih/nlm/ncbi/ngs/LMProperties.java \
+		gov/nih/nlm/ncbi/ngs/Logger.java \
+		gov/nih/nlm/ncbi/ngs/Manager.java \
+		gov/nih/nlm/ncbi/ngs/NGS.java \
+		gov/nih/nlm/ncbi/ngs/Version.java \
+		gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java \
+		gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java \
+		gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java \
+		gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java \
+		-d . -classpath . -sourcepath .:itf:
+	jar cf ngs-java.jar `find . -name "*.class"` || ( ${RM} -f ngs-java.jar && false )
+	javac  \
+		examples/examples/AlignTest.java \
+		examples/examples/AlignSliceTest.java \
+		examples/examples/FragTest.java \
+		examples/examples/PileupTest.java \
+		examples/examples/RefTest.java \
+		examples/examples/ReadGroupTest.java \
+		-d . -classpath . -sourcepath .:itf:gov/nih/nlm/ncbi/ngs
+	jar cf `find examples -name "*.class"` || ( ${RM} -f ngs-examples.jar && false )
+
+clean:
+	${RM} -f \
+		ngs/*.class \
+		ngs/itf/*.class \
+		examples/*.class \
+		gov/nih/nlm/ncbi/ngs/*.class \
+		gov/nih/nlm/ncbi/ngs/error/*.class \
+		gov/nih/nlm/ncbi/ngs/error/cause/*.class \
+		*.jar

ngs-sdk/Makefile.simple

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+
+MAKE	?= make
+DIRS	= adapter dispatch language
+LN	?= ln
+RM	?= rm
+
+all:
+	for dir in ${DIRS}; do \
+	    ${MAKE} -C $$dir -f Makefile.simple ARCH=`uname -p`; \
+	done
+	${CXX} -shared -o ${SO_NAME} ${SO_FLAGS} \
+		*/*.o -L./dispatch -lngs-disp
+	${LN} -f ${SO_NAME} ${SO_SHORT_NAME}
+	${LN} -f ${SO_NAME} libngs-sdk.${SO_EXT}
+
+clean:
+	for dir in ${DIRS}; do \
+	    ${MAKE} -C $$dir -f Makefile.simple clean; \
+	done
+	${RM} -f libngs-sdk.*

ngs-sdk/adapter/Makefile.depend

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+AlignmentItf.o: AlignmentItf.cpp ../ngs/adapter/AlignmentItf.hpp \
+  ../ngs/adapter/FragmentItf.hpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/FragmentItf.h ../ngs/itf/AlignmentItf.h \
+  ../ngs/adapter/StringItf.hpp ../ngs/itf/StringItf.h \
+  ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} AlignmentItf.cpp
+
+ErrBlock.o: ErrBlock.cpp ErrBlock.hpp ../ngs/adapter/ErrorMsg.hpp \
+  ../ngs/itf/ErrBlock.h ../ngs/itf/defs.h
+	${CXX} -c ${CXXFLAGS} ErrBlock.cpp
+
+ErrorMsg.o: ErrorMsg.cpp ../ngs/adapter/ErrorMsg.hpp
+	${CXX} -c ${CXXFLAGS} ErrorMsg.cpp
+
+FragmentItf.o: FragmentItf.cpp ../ngs/adapter/FragmentItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/FragmentItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} FragmentItf.cpp
+
+PileupEventItf.o: PileupEventItf.cpp ../ngs/adapter/PileupEventItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/PileupEventItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/AlignmentItf.hpp \
+  ../ngs/adapter/FragmentItf.hpp ../ngs/itf/FragmentItf.h \
+  ../ngs/itf/AlignmentItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} PileupEventItf.cpp
+
+PileupItf.o: PileupItf.cpp ../ngs/adapter/PileupItf.hpp \
+  ../ngs/adapter/PileupEventItf.hpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/PileupEventItf.h ../ngs/itf/PileupItf.h \
+  ../ngs/adapter/StringItf.hpp ../ngs/itf/StringItf.h \
+  ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} PileupItf.cpp
+
+ReadCollectionItf.o: ReadCollectionItf.cpp \
+  ../ngs/adapter/ReadCollectionItf.hpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/ReadCollectionItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/ReadGroupItf.hpp \
+  ../ngs/itf/ReadGroupItf.h ../ngs/adapter/ReferenceItf.hpp \
+  ../ngs/itf/ReferenceItf.h ../ngs/adapter/AlignmentItf.hpp \
+  ../ngs/adapter/FragmentItf.hpp ../ngs/itf/FragmentItf.h \
+  ../ngs/itf/AlignmentItf.h ../ngs/adapter/ReadItf.hpp \
+  ../ngs/itf/ReadItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} ReadCollectionItf.cpp
+
+ReadGroupItf.o: ReadGroupItf.cpp ../ngs/adapter/ReadGroupItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/ReadGroupItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/StatisticsItf.hpp \
+  ../ngs/itf/StatisticsItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} ReadGroupItf.cpp
+
+ReadItf.o: ReadItf.cpp ../ngs/adapter/ReadItf.hpp \
+  ../ngs/adapter/FragmentItf.hpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/FragmentItf.h ../ngs/itf/ReadItf.h \
+  ../ngs/adapter/StringItf.hpp ../ngs/itf/StringItf.h \
+  ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} ReadItf.cpp
+
+Refcount.o: Refcount.cpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/adapter/StringItf.hpp ../ngs/itf/StringItf.h \
+  ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} Refcount.cpp
+
+ReferenceItf.o: ReferenceItf.cpp ../ngs/adapter/ReferenceItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/ReferenceItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/StatisticsItf.hpp \
+  ../ngs/itf/StatisticsItf.h ../ngs/adapter/AlignmentItf.hpp \
+  ../ngs/adapter/FragmentItf.hpp ../ngs/itf/FragmentItf.h \
+  ../ngs/itf/AlignmentItf.h ../ngs/adapter/PileupItf.hpp \
+  ../ngs/adapter/PileupEventItf.hpp ../ngs/itf/PileupEventItf.h \
+  ../ngs/itf/PileupItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} ReferenceItf.cpp
+
+ReferenceSequenceItf.o: ReferenceSequenceItf.cpp \
+  ../ngs/adapter/ReferenceSequenceItf.hpp ../ngs/adapter/Refcount.hpp \
+  ../ngs/itf/Refcount.h ../ngs/itf/VTable.h ../ngs/itf/defs.h \
+  ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/ReferenceSequenceItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} ReferenceSequenceItf.cpp
+
+StatisticsItf.o: StatisticsItf.cpp ../ngs/adapter/StatisticsItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/StatisticsItf.h ../ngs/adapter/StringItf.hpp \
+  ../ngs/itf/StringItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} StatisticsItf.cpp
+
+StringItf.o: StringItf.cpp ../ngs/adapter/StringItf.hpp \
+  ../ngs/adapter/Refcount.hpp ../ngs/itf/Refcount.h ../ngs/itf/VTable.h \
+  ../ngs/itf/defs.h ../ngs/adapter/defs.h ../ngs/unix/x86_64/atomic32.h \
+  ../ngs/itf/StringItf.h ../ngs/adapter/ErrorMsg.hpp ErrBlock.hpp \
+  ../ngs/itf/ErrBlock.h
+	${CXX} -c ${CXXFLAGS} StringItf.cpp
+