BioShell is written in C++11 and must be built before use. This is a quite easy process, which requires CMake ( 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 ( from Bitbucket:

git clone
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