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INSTALL.md

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kallisto installation

Requirements

  • CMake version >= 2.8.12
    • Can be installed via homebrew: brew install cmake
  • zlib (should be installed on OSX >= 10.9)
  • HDF5 C libraries

Installation

  1. First clone the repository:

    git clone https://github.com/pachterlab/kallisto.git

  2. Move to the source directory:

    cd kallisto

  3. Make a build directory and move there

    mkdir build
cd build

  4. Execute cmake. There are a few options:

    • -DBUILD_TESTING=ON builds tests (off by default)
    • -DCMAKE_INSTALL_PREFIX:PATH=$HOME which will put kallisto in $HOME/bin as opposed to the default (/usr/local/bin)
    cmake ..

    This is only required when one of the CMakeLists.txt files changes or new source files are introduced. It will make a new set of Makefiles

  5. Build the code

    make

    Optionally install into the cmake install prefix path:

    make install

  6. Run the code. The source tree hierarchy is copied, so you can find kallisto at src/kallisto and tests at test/tests.

After performing these steps, you can simply build using make as long as new source files aren't introduced or the CMakeLists.txt scripts aren't modified.