Moved PacBio, prepare, ufasta, quorum, SuperReads, and SOAPdenovo2 mo…

…dule into a global compilation module

.gitignore

@@ -1,2 +1,12 @@
 autom4te.cache
 build
+*.in
+config.*
+aclocal.m4
+configure
+depcomp
+install-sh
+missing
+autom4te.cache
+ltmain.sh
+compile

Makefile

@@ -4,17 +4,19 @@ VERSION = 3.0.1
 NCPU = $(shell grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl hw.ncpu 2>/dev/null || echo 1)
 
 # Component versions
-COMPONENTS = jellyfish SuperReads quorum PacBio CA CA8 SOAPdenovo2 prepare ufasta
+COMPONENTS = jellyfish CA CA8 global # PacBio prepare ufasta quorum SuperReads SOAPdenovo2
 
 ##################################################################
 # Rules for compilling a working distribution in build (or DEST) #
 ##################################################################
 UPD_INSTALL = $(shell which install) -C
 PWD = $(shell pwd)
 PREF ?= $(PWD)
+# PREF ?= .
 BUILDDIR ?= $(PREF)/build
 SUBDIRS = $(foreach i,$(COMPONENTS),$(BUILDDIR)/$(i))
 check_config = test -f $@/Makefile -a $@/Makefile -nt $(1)/configure.ac || (cd $@; $(PWD)/$(1)/configure --prefix=$(BUILDDIR)/inst $(2))
+global_config = test -f $@/Makefile -a $@/Makefile -nt configure.ac || (cd $@; $(PWD)/configure --prefix=$(BUILDDIR)/inst $(1))
 make_install = $(MAKE) -C $@ -j $(NCPU) install INSTALL="$(UPD_INSTALL)"
 
 # Get info of where things are installed
@@ -36,24 +38,34 @@ $(BUILDDIR)/jellyfish: jellyfish/configure
 	$(call check_config,jellyfish,--program-suffix=-2.0)
 	$(call make_install)
 
-$(BUILDDIR)/SuperReads: SuperReads/configure
-	mkdir -p $@
-	$(call check_config,SuperReads,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
-	$(call make_install)
+# $(BUILDDIR)/SuperReads: SuperReads/configure
+# 	mkdir -p $@
+# 	$(call check_config,SuperReads,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
+# 	$(call make_install)
 
-$(BUILDDIR)/quorum: quorum/configure
-	mkdir -p $@
-	$(call check_config,quorum,--enable-relative-paths JELLYFISH=$(BINDIR)/jellyfish-2.0 PKG_CONFIG_PATH=$(PKGCONFIGDIR))
-	$(call make_install)
+# $(BUILDDIR)/quorum: quorum/configure
+# 	mkdir -p $@
+# 	$(call check_config,quorum,--enable-relative-paths JELLYFISH=$(BINDIR)/jellyfish-2.0 PKG_CONFIG_PATH=$(PKGCONFIGDIR))
+# 	$(call make_install)
 
-$(BUILDDIR)/PacBio: PacBio/configure
-	mkdir -p $@
-	$(call check_config,PacBio,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
-	$(call make_install)
+# $(BUILDDIR)/PacBio: PacBio/configure
+# 	mkdir -p $@
+# 	$(call check_config,PacBio,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
+# 	$(call make_install)
 
-$(BUILDDIR)/ufasta: ufasta/configure
+# $(BUILDDIR)/ufasta: ufasta/configure
+# 	mkdir -p $@
+# 	$(call check_config,ufasta,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
+# 	$(call make_install)
+
+# $(BUILDDIR)/prepare: prepare/configure
+# 	mkdir -p $@
+# 	$(call check_config,prepare,)
+# 	$(call make_install)
+
+$(BUILDDIR)/global: ./configure
 	mkdir -p $@
-	$(call check_config,ufasta,PKG_CONFIG_PATH=$(PKGCONFIGDIR))
+	$(call global_config,PKG_CONFIG_PATH=$(PKGCONFIGDIR) --enable-relative-paths JELLYFISH=$(BINDIR)/jellyfish-2.0)
 	$(call make_install)
 
 $(BUILDDIR)/CA: CA/build-default/tup.config CA/.tup/db
@@ -76,14 +88,9 @@ CA/build-default/tup.config:
 	 echo -n "CONFIG_JELLYFISH_LIBS="; pkg-config --libs jellyfish-2.0 \
 	) > $@
 
-$(BUILDDIR)/prepare: prepare/configure
-	mkdir -p $@
-	$(call check_config,prepare,)
-	$(call make_install)
-
-$(BUILDDIR)/SOAPdenovo2: SOAPdenovo2/build-default/tup.config SOAPdenovo2/.tup/db
-	cd SOAPdenovo2; tup upd
-	mkdir -p $(BUILDDIR)/inst/bin; install -t $(BUILDDIR)/inst/bin -C SOAPdenovo2/build-default/SOAPdenovo-63mer SOAPdenovo2/build-default/SOAPdenovo-127mer
+# $(BUILDDIR)/SOAPdenovo2: SOAPdenovo2/build-default/tup.config SOAPdenovo2/.tup/db
+# 	cd SOAPdenovo2; tup upd
+# 	mkdir -p $(BUILDDIR)/inst/bin; install -t $(BUILDDIR)/inst/bin -C SOAPdenovo2/build-default/SOAPdenovo-63mer SOAPdenovo2/build-default/SOAPdenovo-127mer
 
 SOAPdenovo2/build-default/tup.config:
 	mkdir -p $(dir $@)
@@ -122,6 +129,10 @@ clean_distdir:
 $(DISTDIST)/%:
 	$(MAKE) -C $(BUILDDIR)/$* -j $(NCPU) distdir distdir="$@"
 
+$(DISTDIST)/global:
+	#$(MAKE) -C $(BUILDDIR)/global -j $(NCPU) distdir distdir=$(DISTDIST)
+	cd $(BUILDDIR)/global; make -j $(NCPU) dist && tar zxf global*.tar.gz -C $(DISTDIST)
+
 # For the module that do not support 'make distdir', get a verbatim copy from git
 define GIT_TAR =
 $(DISTDIST)/$1:

Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = prepare ufasta PacBio quorum SuperReads SOAPdenovo2

configure.ac

@@ -0,0 +1,88 @@
+AC_INIT([global], [1], [gmarcais@umd.edu])
+AC_CANONICAL_HOST
+AC_CONFIG_MACRO_DIR([m4])
+AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])
+AM_SILENT_RULES([yes])
+AC_CONFIG_SRCDIR([.])
+AC_CONFIG_HEADERS([config.h])
+AC_PROG_LIBTOOL
+
+# Change default compilation flags
+AC_SUBST([ALL_CXXFLAGS], [-std=c++0x])
+CXXFLAGS="-std=c++0x $CXXFLAGS"
+AC_LANG(C++)
+AC_PROG_CC
+AC_PROG_CXX
+
+# Checks for libraries.
+AC_CHECK_LIB([pthread], [pthread_create])
+AC_SEARCH_LIBS([clock_gettime], [rt], [AC_DEFINE([HAVE_CLOCK_GETTIME], [1], [Define to 1 if you have the `clock_gettime' function])])
+
+# Checks for Jellyfish module
+PKG_CHECK_MODULES([JELLYFISH2_0], [jellyfish-2.0])
+JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-2.0)
+AC_SUBST([JELLYFISH_VERSION])
+AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to looking in PATH)])
+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish], [false])])
+
+# On MacOS X, use _NSGetExecutablePath to find path to own executable
+AC_MSG_CHECKING([for _NSGetExecutablePath])
+AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <mach-o/dyld.h>]],
+                                   [[_NSGetExecutablePath(0, 0);]])],
+                  [AC_MSG_RESULT([yes])]
+                  [AC_DEFINE([HAVE_NSGETEXECUTABLEPATH], [1], [Used to find executable path on MacOS X])],
+                  [AC_MSG_RESULT([no])])
+
+# AC_CHECK_LIB(boost_regex, toto)
+AC_MSG_CHECKING([for libboost_regex])
+AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <boost/regex.hpp>],
+                                [boost::regex regexp])],
+                                [AC_MSG_RESULT([yes])] [AC_DEFINE([HAVE_BOOST_REGEX], 1, [Have libboost_regex])]
+                                                       [have_boost=true],
+                                [AC_MSG_RESULT([no])]
+                                [have_boost=false])
+AM_CONDITIONAL([BOOST_REGEX], [test x$have_boost = xtrue])
+
+# Checks for library functions.
+AC_FUNC_MMAP
+AC_CHECK_FUNCS([mremap])
+
+# Use valgrind to check memory allocation with mmap
+AC_ARG_ENABLE([valgrind],
+              [AS_HELP_STRING([--enable-valgrind], [Instrument mmap memory allocation with valgrind])])
+AS_IF([test "x$enable_valgrind" = xyes],
+      [AC_DEFINE([HAVE_VALGRIND], [1], [Define is using Valgrind])]
+      [PKG_CHECK_MODULES([VALGRIND], [valgrind >= 1.8.0])])
+
+# Check for builtin functions
+AC_MSG_CHECKING([for __builtin_prefetch])
+AC_LINK_IFELSE([AC_LANG_PROGRAM([[int x = 0;]],
+                                [[__builtin_prefetch(&x);]])],
+               [AC_MSG_RESULT([yes])]
+               [AC_DEFINE([HAVE_BUILTIN_PREFETCH], [1], [Defined if __builtin_prefetch is supported])],
+               [AC_MSG_RESULT([no])])
+
+# From Quorum
+# --enable-relative-paths
+AC_ARG_ENABLE([relative-paths],
+              [AC_HELP_STRING([--enable-relative-paths], [store relative paths in quorum Perl script])])
+AM_CONDITIONAL([RELATIVE_PATHS], [test x$enable_relative_paths = xyes])
+
+# --with-relative-jf-path
+AC_ARG_WITH([relative-jf-path],
+            [AC_HELP_STRING([--with-relative-jf-path], [relative path from quorum to jellyfish (use an absolute path if not given. default to "." if given with no argument)])],
+            [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;; esac],
+            [with_relative_jf_path= ])
+AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
+AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
+
+AC_CHECK_TYPE([__int128],
+              [AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])])
+
+
+# Check for yaggo
+AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])
+AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])])
+
+AC_CONFIG_FILES([Makefile prepare/Makefile ufasta/Makefile PacBio/Makefile quorum/Makefile SuperReads/Makefile SOAPdenovo2/Makefile])
+AC_OUTPUT

install.sh.in

@@ -25,15 +25,18 @@ BINDIR=$(make -s -C $JF_DIR print-bindir)
 LIBDIR=$(make -s -C $JF_DIR print-libdir)
 PATH="$BINDIR:$PATH"
 
+(cd global-1 && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
+
 (cd CA/src && make LD_RUN_PATH="$LIBDIR")
 (cd CA8/kmer && make install)
 (cd CA8/samtools && make)
 (cd CA8/src && make)
-(cd $SR_DIR && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
-(cd $QR_DIR && ./configure --prefix=$DEST --enable-relative-paths && make -j $NUM_THREADS install)
-(cd PacBio  && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
-(cd SOAPdenovo2 && make --eval="debug=true" && install -t "$BINDIR" SOAPdenovo-63mer SOAPdenovo-127mer)
-(cd prepare && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
+
+# (cd $SR_DIR && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
+# (cd $QR_DIR && ./configure --prefix=$DEST --enable-relative-paths && make -j $NUM_THREADS install)
+# (cd PacBio  && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
+# (cd SOAPdenovo2 && make --eval="debug=true" && install -t "$BINDIR" SOAPdenovo-63mer SOAPdenovo-127mer)
+# (cd prepare && ./configure --prefix=$DEST && make -j $NUM_THREADS install)
 
 if [ "$ROOT" != "$DEST" ]; then
     for i in CA CA8; do