# -------------------------------------------------------------------
# LHOTSE: Toolbox for adaptive statistical models
# -------------------------------------------------------------------
# Module: GLOBAL
# Desc.:  Template for system-dependent part of Makefile
# -------------------------------------------------------------------

# -------------------------------------------------------------------
# This file contains system-dependent variables, it is included by
# the main Makefile.
#
# You need to specialize this template to your system. The default
# way is:
# - Copy this file to make.inc.def
# - Edit make.inc.def, specializing it to your system
#
# If you repeatedly compile the LHOTSE sources on different systems,
# the following alternative may be useful:
# - For a system, pick a novel identifier $$$ (lower-case; replace
#   $$$ by the identifier in what follows), such that make.inc.$$$
#   does not already exist
# - Copy this file to make.inc.$$$, edit it to specialize it to the
#   system
# - When calling "make", append the option "where=$$$"
# -------------------------------------------------------------------


# -------------------------------------------------------------------
# ROOTDIR: Main directory
# Absolute path of the project root directory (where the Makefile
# is, and from where the module directories branch off)
# -------------------------------------------------------------------
ROOTDIR=/kyb/agbs/seeger/tex-files/bioinf06/code

# -------------------------------------------------------------------
# CXXINCS, CXXLDOPTS: C/C++ headers, libraries
# On most systems, these variables do not have to be specified, since
# the C++ compiler is configured appropriately. You may want to
# specify it if you run into problems without, or if you want to use
# a compiler different from the standard one on your system. The
# variable value consists of a sequence of "-I<path>" parts.
# For GCC, the C++ headers are typically found in
# /usr/include/c++/<version> and
# /usr/include/c++/<version>/<system>, and the C headers in
# /usr/lib/gcc-lib/<system>/<version>/include.
# The libraries are typically in
# /usr/lib/gcc-lib/<system>/<version>.
# NOTE: On some systems, the C++ headers have to be specified, while
# the C headers and libraries are found automatically.
# -------------------------------------------------------------------
CXXINCS=	-I/usr/include/c++/3.3 -I/usr/include/c++/3.3/i486-linux
#CXXLDOPTS=

# -------------------------------------------------------------------
# CC, CXX: C, C++ Compiler
# The default is "g++" for both values, which correct for GCC.
# Change this if you do not want to use the default compiler on
# your system.
# -------------------------------------------------------------------
#CC=
#CXX=

# -------------------------------------------------------------------
# EXINCS_GSL, EXLDOPTS_GSL: GNU Scientific Library
# The headers for GSL must be in <path>/gsl, where "-I<path>" is
# specified in EXINCS_GSL. If <path> is /usr/include, or
# /usr/local/include, you may not have to specify this variable.
# The static library libgsl.a must be in <path>, where "-L<path>"
# is specified in EXLDOPTS_GSL. If <path> is /usr/lib, or
# /usr/local/lib, you may not have to specify this variable.
#
# Contact your system administrator to find out whether GSL is
# present on your system, and where these files locate. If GSL
# is not present, you have to install it locally. The sources
# can be obtained from:
#   http://www.gnu.org/software/gsl/
# See the LHOTSE installation guide for more details.
# -------------------------------------------------------------------
EXINCS_GSL=	-I/kyb/agbs/seeger/include
EXLDOPTS_GSL=	-L/kyb/agbs/seeger/lib

# -------------------------------------------------------------------
# EXLDOPTS_BLAS, EXLIBS_BLAS: BLAS, LAPACK libraries
# LHOTSE requires the LAPACK library and a local variant of the
# BLAS library, furthermore the CBLAS interface to the latter.
# The static libraries (libXXX.a) are used. EXLDOPTS_BLAS contains
# "-L<path>", s.t. the library files are found in <path>.
# EXLIBS_BLAS contains the library string, a sequence of "l<lib>"
# parts.
# A free implementation of the BLAS which is tuned automatically
# to your machine, is given by ATLAS. If you use ATLAS and LAPACK,
# the recommended EXLIBS_BLAS is:
#   -llapack -lf77blas -lcblas -latlas
# Note that the ordering does matter (see ATLAS documentation for
# details). This is also the def. value of EXLIBS_BLAS, which you
# probably do not have to change here.
#
# Contact your system administrator to find out whether LAPACK and
# a suitable BLAS version are present on your system, and where
# these files locate. Note that on many systems installed
# "by default", the static libraries are missing, or the BLAS
# libraries are not tuned to the machine. It is strongly
# recommended to use a BLAS variant tuned to your machine. ATLAS
# sources can be obtained from:
#   http://math-atlas.sourceforge.net/
# See the LHOTSE installation guide for more details.
# -------------------------------------------------------------------

EXLDOPTS_BLAS=	-L/kyb/agbs/seeger/lib
#EXLIBS_BLAS=

# -------------------------------------------------------------------
# The remainder of this file is not used presently, and no changes
# have to be made there.
# -------------------------------------------------------------------

# -------------------------------------------------------------------
# EXINCS_MATLAB, MATOPTS: Matlab interface
# LHOTSE can be controlled from Matlab through the MATIF interface,
# which uses the MATLAB MEX interface.
# If EXINCS_MATLAB contains "-I<path>", the MATLAB MEX headers must
# be found in <path>.
# MATOPTS are options to be passed to the "mex" command, apart from
# the usual compiler/linker options.
# -------------------------------------------------------------------

EXINCS_MATLAB=	-I/usr/local/matlab65/extern/include
#MATOPTS=

# -------------------------------------------------------------------
# LOCALLIBS_mexstat: MEX files with partial static linkage
# Matlab MEX files are linked into a dynamic library and by def. use
# dynamic libraries only. This can fail on badly configured systems.
# If so, the make option "mex=stat" can be used (see Makefile).
# 
# This option requires LOCALLIBS_mexstat. If mex works for you with
# dynamic libraries, you do not have to specify it.
# Otherwise, you have to specify all external libraries here, the
# ones appearing in LOCALLIBS (Makefile), but explicitly their
# static variants. Instead of
#   -l<libname>
# we need
#   <libname_path>/lib<libname>.a
# The path <libname_path> has to be given explicitly, even if it is
# contained in some "-L" directive.
#
# NOTE: The "-static" directive forces the linker to use static
# libraries. Unfortunately, this directive cannot be use with the
# "mex" command.
# -------------------------------------------------------------------

LLL_TEMP=	/kyb/agbs/seeger/lib/
LLL2_TEMP=	/usr/lib/gcc-lib/i486-linux/3.3.5/
LOCALLIBS_mexstat=	$(LLL_TEMP)libgsl.a $(LLL_TEMP)liblapack.a $(LLL_TEMP)libf77blas.a $(LLL_TEMP)libcblas.a $(LLL_TEMP)libatlas.a /usr/lib/libg2c.a /usr/lib/libm.a
