Installation

BioShell is written in C++11 and must be built before use. This is a quite easy process, which requires CMake (https://cmake.org) and a relatively modern C++ compiler such as gcc 5.0 or clang 10.0 The compilation procedure is as follows:

1. If you haven’t done it yet, clone bioshell-release repository (https://bitbucket.org/dgront/bioshell-release/src/master/) from Bitbucket:

git clone git@bitbucket.org:dgront/bioshell-release.git
cd bioshell-release

This should create bioshell-release directory in your current location. The second line steps into this new directory

  1. Run CMake:

    cd build
    cmake ..
    

    The build directory will contain compilation intermediate files and may be deleted once BioShell is compiled. The first line enters that direcotry, the second command calls cmake to set up the compilation process. CMake attempts to set up everything automatically, sometimes however it would require some guidance, e.g. to find the right compiler (see below)

  2. Run Make:

    make -j 4
    

    where -j 4 allows make use 4 cores to run parallel compilations

  3. Additional parameters for compilation

The procedure described above compiles the package with the default settings: Release build with no profiling. To change it, you should remove everything from ./build directory and generate new makefiles with new settings:

  • in order to use a compiler other that the default one (e.g. gcc version 4.8), say:

    cmake -DCMAKE_CXX_COMPILER=g++-4.8  -DCMAKE_C_COMPILER=gcc-4.8 -DCMAKE_BUILD_TYPE=Release ..
    

or to use icc for instance:

cmake -DCMAKE_CXX_COMPILER=icc  -DCMAKE_C_COMPILER=icc -DCMAKE_BUILD_TYPE=Release ..
  1. Using IDE

In the above examples, cmake was used to produce makefiles for to compile BioShell. cmake command may be also used to generate project files for other environments, in particular:

  • to produce *.xcodeproj file for xcode:

    cmake  -DCMAKE_BUILD_TYPE=Release -G Xcode
    
  • or to prepare solution files for Microsoft Visual Studio (must be run on a Windows machine):

    cmake  -DCMAKE_BUILD_TYPE=Release -G "Visual Studio 2013"