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Manual Installation

If you wish to install HATCHet directly from this repository, the steps are a bit more involved. The core module of HATCHet is written in C++11 and thus requires a modern C++ compiler (GCC >= 4.8.1, or Clang). As long as you have a recent version of GCC or Clang installed, setuptools should automatically be able to download a recent version of cmake and compile the Hatchet code into a working package.

The installation process can be broken down into the following steps:

  1. Get Gurobi (>= 6.0)

    The coordinate-method applied by HATCHet is based on several integer linear programming (ILP) formulations. Gurobi is a commercial ILP solver with two licensing options: (1) a single-host license where the license is tied to a single computer and (2) a network license for use in a compute cluster (using a license server in the cluster). Both options are freely and easily available for users in academia. Download Gurobi for your specific platform.

  2. Set GUROBI_HOME environment variable

    $ export GUROBI_HOME=/path/to/gurobiXXX

    Set GUROBI_HOME to where you download Gurobi. Here XXX is the 3-digit version of gurobi.

  3. Build Gurobi

    $ cd "${GUROBI_HOME}"
$ cd linux64/src/build/
$ make
$ cp libgurobi_c++.a ../../lib

    Substitute mac64 for linux64 if using the Mac OSX platform.

  4. Create a new venv/conda environment for Hatchet

    Hatchet is a Python 3 package. Unless you want to compile/install it in your default Python 3 environment, you will want to create either a new Conda environment for Python 3 and activate it:

    conda create --name hatchet python=3.8
conda activate hatchet

    or use virtualenv through pip:

    python3 -m pip virtualenv env
source env/bin/activate

  5. Install basic packages

    It is highly recommended that you upgrade your pip and setuptools versions to the latest, using:

    pip install -U pip
pip install -U setuptools

  6. Build and install HATCHet

    Execute the following commands from the root of HATCHet's repository.

    $ pip install .

    NOTE: If you experience a failure of compilation with an error message like:

    _undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'_.

    you may need to set CXXFLAGS to -pthread before invoking the command:

    $ CXXFLAGS=-pthread pip install .

    When the compilation process fails or when the environment has special requirements, you may have to manually specify the required paths to Gurobi by following the detailed intructions.

  7. Install required utilities

    For reading BAM files, read counting, allele counting, and SNP calling, you need to install SAMtools and BCFtools.