Installing / Building Genome Workbench

Windows 2000 / XP / Vista / 7 (64-bit)

The Windows 2000/XP package is a native Windows installer. Once you have downloaded the installer executable, simply double-click it in Windows Explorer to launch this. The installation wizard will then walk you through the steps of installing the main executable and registering its components.

Once Genome Workbench is installed, you should have an icon on your desktop and an item in your start menu to launch Genome Workbench.

MacOS X

The MacOS X package is an executable disk image. Once you have downloaded this image, you should be able to launch the application by double-clicking on it in the Finder.

We provide only one package for MacOS X, and that package is designed to work on MacOS X 10.6 and later (Snow Leopard and Lion).  MacOS X 10.5 and earlier are no longer supported.

Linux

The Linux package is provided for 32-bit and 64-bit Intel platforms in a variety of packaging formats, including binary RPM, DEB, and TGZ packages. We compile and test at NCBI using Fedora 18 (rpm packages) and Ubuntu 12.04 (deb and tgz packages). The provided .rpm and .deb packages should work according to your distribution's installation procedures. The .tgz tarball can be unzipped into the root of the file system, and will install the software into /opt/ncbi/gbench-2.X.X Once unpacked, you should add the path /opt/ncbi/gbench-2.X.X to the global or user path to gain execution access. Replace 2.X.X with the current version of the application. Genome Workbench can then be executed using the gbench script file, also located in the bin/ subdirectory. It is recommended that this bin/ directory be added to users's $PATH variable for ease of execution. On Ubuntu Genome Workbench application entry is added to Other group of the applications menu.

Example 32-bit tarball install:

  (as root, unpack:)
  #cd /
  #tar xzvf .../gbench-linux-Ubuntu-i386-2.7.5.tgz

  (as a user, execute:)
  /opt/ncbi/gbench-2.7.5/bin/gbench

  (from a path variable:)
  export PATH=$PATH:/opt/ncbi/gbench-2.7.5/bin
  gbench

Source Installations

Genome Workbench is also provided in source form. The source package is placed in the public domain, and is freely available for anyone to modify and redistribute, in either binary or source form. Details of the NCBI Public Domain License can be found here.

Genome Workbench makes use of the NCBI C++ Toolkit. A subset of the public toolkit source code is included in the Genome Workbench source package. While the latest versions of Genome Workbench can be found here, Genome Workbench is also available as part of the NCBI C++ Toolkit's public releases.

The essentials of the build process are documented as part of the NCBI C++ Toolkit. There are a couple of specific details that should be remembered when building Genome Workbench:

  • In order to build Genome Workbench successfully, you must choose a multithreaded DLL build.
    • For Unix/Linux, a build script (build-linux-distro.sh) is provided in the root directory of the source tarball. This script is the script we use for building distributions in-house, and will automatically ensure that the wxWidgets libraries are built and installed side-by-side with the application. This dual installation ensures that the application will maintain binary compatibility through system upgrades. Please, check README.LINUX for more information for the Linux/Unix builds.
    • For Windows, please use the Visual Studio solution named ncbi_gbench.sln, located in compilers/msvc800_prj/dll/build/gbench.
    • The build for MacOS X supports two versions of the build system: the command-line 'configure'-based solution, as described for Unix builds; and a build system for xCode (in compilers/xCode).
  • Genome Workbench requires a multithreaded environment.
    • In Unix / Linux, you should supply the --with-mt flag to 'configure'. This is implied by --with-gbench.
    • In Windows, you should use ReleaseDLL or DebugDLL build settings, generated by the solution configure process.
  • Genome Workbench makes use of several third-party libraries. These include:
    • wxWidgets version 2.9.4 or higher, a cross-platform windowing toolkit. We require that wxWidgets be compiled with certain flags to support execution, including --with-opengl --disable-monolithic --disable-sockets (and for mac only:) --with-osx_cocoa
    • SQLite, version 3.6 or higher.
    • BerkeleyDB, of at least version 4.5
    • Various image libraries: libpng, libjpeg, libtiff, and giflib
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Last updated: 2014-08-21T14:02:42-04:00