source: branches/0.15-stable/README

Last change on this file was 3666, checked in by peter, 5 months ago

configure.ac: add --disable-cxx11 in --help output

Change default behaviour of configure. If neither --enable-cxx11 nor
--disable-cxx11 is given, try c++11 features with CXX but if it
doesn't work, don't try with list of compiler options (as is behaviour
with --enable-cxx11).

README: update text to match behaviour

yat/utility/config_public.h.in: extend docs

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$Id: README 3666 2017-07-25 08:09:23Z peter $

About yat

This directory contains the yat library. For an overview of the project, visit

http://dev.thep.lu.se/yat

Configuring and building yat

  1. If you checked out this project from the subversion repository you must run 'bootstrap' to initialize the build system.
  2. Issue './configure' to create the Makefiles. Optionally run configure with '--enable-debug', which will turn on debug options.
  3. Compile with 'make'.
  4. 'make doc' will generate documentation.
  5. Optionally do 'make check' to run test programs.
  6. Issue 'make install' to install the package on your system, documentation will not be installed if documentation was not generated above. Default installation location is /usr/local; this can be changed with './configure --prefix=/dir/to/install/to'.
  7. Optionally do 'make installcheck' to verify that intallation completed correctly.

The configure script has additional options; ./configure --help will offer you those choices or refer to Requirements below.

Requirements

Except for the obviously needed C++ compiler there are a few packages and programs required for compiling yat and generate supporting material. The configure script will look for required programs and report failure to meet the requirements. Here we list some of the requirements, but omit required standard utilities such as echo and sed since these are normally available.

Required packages

GSL

GNU Scientific Library, GSL version 1.8 or later. If you have GSL installed in a non-standard location, ./configure --with-gsl=DIR can be useful to provide the location of GSL. The gsl-config script, which is used to retrieve needed compiler and linker flags, is expected to be found in DIR/bin/. The check for existing GSL can be turned off with option --without-gsl. This can be useful, for example, if gsl-config is not available at configure time but header file will be available at make time.

BLAS

A C implementation of Basic Linear Algebra Subprograms (BLAS) is required. GSL comes with a reference implementation, but you should consider getting a hardware optimized implementation. ATLAS provides optimized BLAS (see below).

The configure script searches for many different BLAS libraries in a specific order (for details refer to m4/yat_cblas.m4). If you want to use a specific CBLAS library, ./configure --with-cblas=LIB may be useful. Note, however, that the chosen/detected CBLAS library is not hard-coded into the installed libyat, but a user can choose a different CBLAS when she links her application. A way to access which CBLAS was detected during the configuration is to access the yat-config script directly or via the autoconf macros included in the distribution. If you do want to hard-code a choice of CBLAS into the installed libyat, you may provide the appropriate value to LIBS. The following line, for example:

#> ./configure LIBS=-lcblas

will hard-code the choice of -lcblas into libyat.

Boost

Boost version 1.35 or later. If you have Boost installed in a non-standard location, ./configure --with-boost=DIR can be useful to provide the location of Boost. Boost header files are expected to be found in DIR/include/ and boost libraries are expected to be found in DIR/lib/. The configure script tries to detect libraries boost_thread and boost_thread. The name of a boost library typically depends on its configuration (see boost's naming convention) and there may be several versions/configurations of the same library installed. The configure tries to pick one of the available libraries, wchih can be overridden with `./configure --with-boost-thread=foo and configure --with-boost-system=foo`, respectively. The check for boost can be turned off with --without-boost.

quiet nan

Quiet NaN's must be supported.

infinity

infinity for type double must be supported.

Optional packages

HTSLIB and Samtools

In order to enable functionality related to bam files, either htslib (http://www.htslib.org) or its predecessor samtools (http://samtools.sourceforge.net) must be available. Header file <sam.h> is required as well as either 'libhts' or 'libbam'. The configure script will try to detect whether <sam.h> is available as 'sam.h', 'htslib/sam.h', 'bam/sam.h', or 'samtools/sam.h'. If you have header files installed outside compiler's search path, you can help the compiler with ./configure CPPFLAGS=-I<include dir> when header files are found in directory <include dir>. Configure detects whether header files are from htslib or old samtools and looks for either libhts or libbam accordingly. If library is installed outside linker's search path, in <libdir>, you can run `./configure LDFLAGS=-L<lib dir>. You can build yat without bam support by running ./configure --without-samtools`.

The samtools program (version 1.2 or newer) is needed for some tests related to bam functionality. If samtools is not found by configure, these tests will be skipped. If you have samtools available outside PATH, you can help configure to find it with `./configure SAMTOOLS=/path/to/samtools`.

ZLIB

Zlib available from http://www.zlib.net/ is required to build samtools and consequently needed to build yat too, unless you turn off samtools support (please refer to samtools section above). Header file zlib.h and library libz are required. If installed in an unconventional location you can help the compiler/linker with `CPPFLAGS=-I<include dir> and LDFLAGS=-L<lib dir>`, respectively.

ATLAS

GSL supplies a reference implementation of BLAS. You may want to consider using hardware optimized BLAS. The ATLAS software provides an automatic hardware optimized BLAS library.

The detection of ATLAS is supported by the yat configuration script but in many cases the ATLAS libraries are installed in non-conventional directory locations. As an example, on Fedora 8, ATLAS libraries are located in /usr/lib/atlas or /usr/lib64/atlas depending on your hardware architecture. If you have ATLAS installed and the configure script fails to locate it, try to add the location to the atlas libraries when running configure:

#> ./configure LDFLAGS="-L/usr/lib64/atlas"

C++11 Features

If enabled, yat uses C++11 features such as rvalues and std::atomic, which make the library faster and safer. You can turn off these features with option

#> ./configure --disable-cxx11

Otherwise the configure script will check if compiler supports rvalue and other features and #define macros as appropriate. In addition, if you run configure with option

#> ./configure --enable-cxx11

the script will first try the features by default, and if not working try a list of different options, such as '-std=cxx11' to turn on support, and if any of them work, #define macros as appropriate in file 'yat/utility/config_public.h' and save compiler option to $CXX, so the library is built with this option.

If you want to use these features in your own code, you need turn them on by #defining YAT_WITH_CXX11 (and make sure the compiler supports them). Please see file 'yat/utility/config_public.h.in' for more discussion how to use macros YAT_WITH_CXX11 and YAT_WITHOUT_CXX11.

Doxygen

Doxygen 1.5 (or newer) is required for generation of the API documentation. If doxygen application is missing, generation of API documentation is disabled.

Documentation

The API documentation for the latest release is available in HTML and can be found through http://dev.thep.lu.se/yat. If you wish to build a local copy, issue make doc and you will find the documents in directory doc/html/.

Developers

See file README.developer for developer specific information.

Mac OS X

On Mac OS X you can create a universal library, a library that works on multiple systems. You can do this by specifying multiple -arch options to the compiler (but not to the preprocessor):

#> ./configure CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \

CXXCPP="g++ -E" --disable-dependency-tracking

This will produce a universal yat library with 4 architectures. If your OS X does not support both Power-PC and Intel-based processors, you can omit these architectures. Also, required libraries, GSL and CBLAS, need to be available as universal libraries with desired architectures.


Copyright (C) 2003 Jari Häkkinen, Peter Johansson
Copyright (C) 2004 Jari Häkkinen
Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017 Peter Johansson
This file is part of yat library, http://dev.thep.lu.se/yat
The yat library 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.
The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
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