COPASI

Linux

Prerequisits

Compiler

You will need gcc 3 or gcc 4.

Libraries

  • QT 4 The binary packages are statically linked against QT 4.5, but all version of QT 4 newer than 4.5 should work. If you only intend to build a non-GUI version of COPASI, Qt 4 version older than 4.5 should work as well as long as qmake is available. If you have a recent linux distribution, Qt 4.5 might already be preinstalled or there will be packages that can be installed. Since Qt 4 is usually distributed as several packages, make sure the development tools and the headers files are installed.
  • LAPACK, CLAPACK, or Intel MKL The binary packages are statically linked against Intel MKL. Just grab the latest version you can find and you should be fine
  • Expat The binary packages are statically linked against 2.0.1, older version will usually work, but you might miss out on some bugfixes. Usually the version that comes with your linux distribution should do.
  • libsbml COPASI up to Build 32 is using a patched version of libsbml 3.4.1 which contains some bugfixes from libsbml 4. We build libsbml without support for reading and writing of compressed files. If you want file compression, you have additional dependencies to zlib and the bzip2 library. libsbml has to be compiled with support for the SBML layout extension. (./configure --enable-layout=yes --enable-compression=no --with-expat). Starting with COPASI Build 33, we switched to libsbml 4 (currently libsbml 4.1.0). The libsbml sources have to be patched to provide support for the SBML render extension which is now supported in COPASI. The patch can be downloaded here. You need to enable the render extension ion libsbml with the --enable-render option.
  • raptor The latest version of this RDF parsing library should be OK. We are currently using version 1.4.19. The version we are using is build against expat and without www support. (configure options --with-xml-parser=expat --with-www=none). If you are using a version that comes with your linux distribution, it will probably be compiled against libxml2 and you will have to include this dependency into COPASI build system before COPASI will compile.

additional library dependencies for the GUI version

  • Qt 4 was already mentioned above, but if you want to build the GUI version, you have to make sure that Qt 4 has been build with Qt 3 compatibility support since parts of the GUI have not been fully converted to Qt 4 yet. This will hopefully change soon.
  • Qwt Just get the latest version and make sure it is compiled against Qt 4
  • QwtPlot3D Get the latest version of this 3D plotting library and make sure it is compiled against Qt 4.
  • SBW Systems Biology Workbench allows us to send and receive SBML models from other SBW enabled programs. The latest version should be OK. COPASI can also be build without SBW support.

Build Steps

  1. Download the source installation package.
  2. Expand the contents of the tarball into a directory of your choice with tar -xzvf Copasi-*-SRC.tar.gz.
  3. Change to the newly created copasi-*-src directory.
  4. Run configure, you will probably need to specify some of the following options:
    Optional Features:
      --enable-debug enable debug build (default: enabled)
      --enable-release enable release build (disables debug, default: disabled)
      --enable-static enable static linkage (default: disabled)
      --enable-gui enable build of GUI (default: enabled, starting with Build 20)
    Required Packages:
      --with-expat=PATH Path to Expat XML Library
      --with-sbml=PATH Path to SBML Library
      --with-qwt=PATH Path to QWT Library
      --with-qwt3d=PATH Path to QWTPlot3D Library
      --with-raptor=PATH Path to raptor Library
    Optional Packages
      --with-clapack=PATH Path to CLAPACK Library
      --with-lapack=PATH Path to LAPACK Library
      --with-mkl=PATH Path to MKL Library
      --with-sbw=PATH Path to SBW Library
To get a full list of configure options, please run "./configure --help".

The configure options for LAPACK, CLAPACK and MKL are mutually exclusive, you must use exactly one of them.

In addition configure recognizes the following environment variables: CFLAGS, CXXFLAGS, LDFLAGS, and QMAKE_ARG (additional arguments provides to qmake).
  1. Run make
  2. Optionally, run make install. This will create a tar ball similar to the dowloadable packages.