2. Installation

BEDOPS is available to users as pre-built binaries and source code.

2.1. Via pre-built packages

Pre-built binaries offer the easiest and fastest installation option for users of BEDOPS. At this time, we offer binaries for 32- and 64-bit versions of Linux and OS X (Intel) platforms.

2.1.1. Linux

1. Download the current 32- or 64-bit package for Linux from Github BEDOPS Releases.

2. Extract the package to a location of your choice. In the case of 32-bit Linux:

   $ tar jxvf bedops_linux_i386-vx.y.z.tar.bz2
   

   In the case of 64-bit Linux:

   $ tar jxvf bedops_linux_x86_64-vx.y.z.tar.bz2
   

   Replace x, y and z with the version number of BEDOPS you have downloaded.

3. Copy the extracted binaries to a location of your choice which is in your environment’s PATH, e.g. ~/opt/bin:

   $ cp bin/* ~/opt/bin
   

   Change this destination folder, as needed.

2.1.2. Mac OS X

1. Download the current Mac OS X package for BEDOPS from Github BEDOPS Releases.
2. Locate the installer package (usually located in ~/Downloads – this will depend on your web browser configuration):

3. Double-click to open the installer package. It will look something like this:

4. Follow the instructions to install BEDOPS and library dependencies to your Mac. (If you are upgrading from a previous version, components will be overwritten or removed, as needed.)

2.2. Via source code

At this time, compilation of BEDOPS requires GCC 4.7 or greater (which includes support for C++11 features required by core BEDOPS tools).

1. If you do not have GCC 4.7 or greater installed, first do so. You can check this with gcc --version, e.g.:

   $ gcc --version
   gcc (MacPorts gcc47 4.7.3_3+universal) 4.7.3
   ...
   

   For Mac OS X users, we recommend first installing Apple Xcode and its Command Line Tools, via the Preferences > Downloads option within Xcode. Then install GCC 4.7 or greater using MacPorts, setting GCC to be the default compiler, e.g.:

   $ sudo port install gcc47
   $ sudo port install gcc_select
   $ sudo port select --set gcc gcc47
   

   In the future, we may provide support for OS X compilation via Clang/LLVM, which is the default compiler included with Xcode.

   For Linux users, use your favorite package manager to install the requisite compiler. For example, in Ubuntu, you might run the following:

   $ sudo apt-get install gcc
   

2. Install a git client of your choice, if you do not already have one installed. Github offers an installation guide.

3. Clone the BEDOPS Git repository in an appropriate local directory:

   $ git clone https://github.com/bedops/bedops.git
   

4. (Linux) Run make static in the top-level of the local copy of the BEDOPS repository:

   $ cd bedops
   $ make static
   

5. (Mac OS X) Run make build_all_darwin_intel_fat in the top-level of the local copy of the BEDOPS repository:

   $ cd bedops
   $ make build_all_darwin_intel_fat
   

6. Install compiled binaries and scripts to a local bin folder:

   $ make install
   

7. Copy the extracted binaries to a location of your choice that is in your environment’s PATH, e.g. ~/opt/bin:

   $ cp bin/* ~/opt/bin
   

   Change this destination folder, as needed.

2.3. Building an OS X installer package for redistribution

1. Follow steps 1-3 and step 5 from the Via Source Code documentation.

2. Run make install_osx_packaging_bins in the top-level of the local copy of the BEDOPS repository:

   $ make install_osx_packaging_bins
   

3. Install WhiteBox Packages.app, an application for building OS X installers, if not already installed.

4. Create a build directory to store the installer and open the BEDOPS.pkgproj file in the top-level of the local copy of the BEDOPS repository, in order to open the BEDOPS installer project, e.g.:

   $ mkdir packaging/os_x/build && open packaging/os_x/BEDOPS.pkgproj
   

   This will open up the installer project with the Packages.app application.

5. Within Packages.app, modify the project to include the current project version number or other desired changes, as applicable.

6. Run the Build > Build menu selection to construct the installer package, located in the packaging/os_x/build subdirectory. Move this installer to the desired location with mv or the OS X Finder.