************ Installation ************ This page describes the installation procedure of EggLib. ------------ Requirements ------------ EggLib is tested under Python 3.7 and above (up to 3.11). Binary distributions are available for MacOSX (10.9+) and Windows (8 or above). If you plan to compile EggLib from source, you'll need the development libraries for your version of Python and possibly the ``htslib`` library (see below). For using any function of the :ref:`wrappers ` module, the corresponding program must be found in your system and EggLib should be configured accordingly (see :ref:`paths`). Other requirements are Python packages ``click`` and ``platformdirs`` for the main package, ``svgwrite``, ``sphinx`` and ``numpydoc`` for generating the documentation and ``scipy`` for running tests. They can all be treated easily by using the package manager **pip**. Dependency on ``htslib`` ======================== The class :class:`~.io.VCF` requires the ``htslib`` external `library `_ with its headers. On major distributions, ``htslib`` can be installed from the package manager (under the name ``htslib-devel`` or ``libhts-dev`` on Ubuntu). EggLib relies on the presence of this library in the system to compile. It is possible to use environment variables to control where the compiler will find the libraries as in the following example:: $ export CPATH=$HOME/.local/include:$CPATH $ export LD_LIBRARY_PATH=$HOME/.local/lib $ export LIBRARY_PATH=$HOME/.local/lib (these commands may be inserted into a bash configuration file such as ``.bashrc``). Note that ``htslib`` is only needed for the class :class:`!VCF`. By default, if ``htslib`` is missing, this class will be skipped. This can be checked through the ``htslib`` flag available in the outpout of the command ``egglib-config infos`` or as the variable ``egglib.config.htslib`` once EggLib is installed. This behaviour can be controlled through the environment variable ``HTSLIB``, which we recommend to set in the local shell only (i.e. not using ``export``) as in the following example:: $ HTSLIB=1 pip install egglib This variable takes three possible values: +------+--------------------------+ | Code | Meaning | +======+==========================+ | 0 | don't require ``htslib`` | +------+--------------------------+ | 1 | require ``htslib`` | +------+--------------------------+ | 2 | flexible mode (default) | +------+--------------------------+ With variable ``HTSLIB=0``, the class :class:`!VCF` is never included. With variable ``HTSLIB=1``, the class :class:`!VCF` is included if compilation and linking to the ``htslib`` library succeeds. If not, an error is displayed. With variable ``HTSLIB=2``, any error occurring while compiling the class :class:`!VCF` is masked and the class is silently skipped. So ``HTSLIB=1`` is recommended if :class:`!VCF` is actually required. Local installation of ``htslib`` ================================ In some cases, it is not possible to install ``htslib``, blocking the installation of EggLib with VCF support. The following recipe is a way to overcome installation restrictions and should be considered as a temporary fix is requesting installation of ``htslib`` using proper means. It has been designed for Linux systems. We will install ``htslib`` locally within the user's home and add local folder to dynamic libraries search paths (and other paths, as shown in the commands below). Install ``htslib`` locally (under ``~/.local``) ----------------------------------------------- This installs ``htslib`` version 1.19.1 (the latest version as of this writing):: $ module load compilers/gcc $ wget https://github.com/samtools/htslib/releases/download/1.19.1/htslib-1.19.1.tar.bz2 $ tar xvf htslib-1.19.1.tar.bz2 $ cd htslib-1.19.1 $ ./configure --prefix=${HOME}/.local $ make $ make install Configure system to include local libraries ------------------------------------------- The following lines should be added to ``${HOME}/.bashrc`` or ``${HOME}/.bash_profile``:: export CPATH=${HOME}/.local/include:${CPATH} export LD_LIBRARY_PATH=$HOME/.local/lib:${LD_LIBRARY_PATH} export LIBRARY_PATH=${HOME}/.local/lib :${LIBRARY_PATH} Changes need to applied using:: $ source ~/.bashrc Install EggLib, making sure it is freshly compiled ================================================== :: $ pip cache purge $ HTSLIB=1 pip --force-reinstall egglib Validate that it worked (the line ``htslib: 1`` should appear):: $ egglib-config infos ------------ Installation ------------ .. highlight:: bash EggLib is on the `Python Package Index `_ and can be installed using **pip** as:: $ pip install egglib --user The ``--user`` flag is not needed in most cases. If the permissions don't allow you to install EggLib in a system-wide location, it will be installed in local user libraries. If the ``pip`` command is not directly accessible or if you want to install EggLib for a specific (non-default) version of Python (for example, 3.11) you can type:: $ python3.11 -m pip install egglib --user or, on Windows, using the Python Launcher:: py -3.11 -m pip install egglib --user You can also: * Select a specific version of EggLib (for example, 3.2.0): ``pip install egglib==3.2.0``. * Upgrade to the latest version: ``pip install --upgrade egglib``. * Remove EggLib: ``pip uninstall egglib``. To generate the documentation, a set of packages are needed which are not required by default. To install those, specify the ``doc`` extra:: $ pip install egglib[doc] --user Similarly, ``scipy`` is needed to run tests. You can either install it yourself or let ``pip`` install it (or check it presence) as a dependency of EggLib:: $ pip install egglib[test] --user Binary packages =============== Binary packages (binary wheels) are available on **pip** for MacOSX and Windows under Python 3.11 or above. **pip** should use the package wheel corresponding to your system. By default, it will attempt to compile EggLib (which is the normal behaviour on Linux). .. note:: Binary packages are not currently supported and won't be available for recent versions of EggLib. Download source and binary packages =================================== The source package can be downloaded from **pip** using:: $ pip download egglib --no-binary :all: This will download the source package. Letting you access the source code. To download the binary package corresponding to your system (assuming it is available), you can just type:: $ pip download egglib Alternatively, all files for the current release are available for download from ``_. Older releases are also archived there. .. _apps: .. note:: Binary packages are not currently supported and won't be available for recent versions of EggLib. --------------------------------- Configuring external applications --------------------------------- If external applications are needed (one is required for every function of the :ref:`wrappers ` module), they must be configured. By default, EggLib will assume that the corresponding programs are absent and will not attempt to run them. Since version 3.2, a companion script in included in the Egglib installation to manage external application paths. To test for the presence of external applications and save the configuration in a user configuration file, issue the following command:: $ egglib-config apps -aLsu * Option ``-a`` launchs autodetection of applications using default command names for invoking them (e.g. ``phyml`` for the PhyML software). If needed, for any application, custom commands can be specified using the ``-c`` option and path to executables can be specified using ``-p``. If a command tries by ``-a`` doesn't work, this application will be left unavailable. * Option ``-L`` displays the result. * Option ``-s`` saves the configuration to a persistent file such as the new configuration will be used by EggLib after subsequent imports. * Option ``-u`` specifies that the configuration file will be saved in a user-specific configuration file. By default, the configuration file is located within the EggLib installation and is erased when EggLib is updated and might require administrator rights for writing. If the user-specific file exists, it is used in priority (so ``-u`` only needs to be specified when it doesn't exist yet). See the manual (``egglib-config apps --help``) for more information. It is also possible to perform these operations using helpers of the :mod:`!wrappers` module, either permanently or temporarily. For details, see :ref:`paths`. ----- Tests ----- Since version 3.2, the test suite is included as a subpackage of EggLib and can be invoked through a companion script named ``egglib-test``. The following command will run all tests and assumes all components (external applications and `htslib`` for the :class:`.io.VCF` class) are available:: $ egglib-test -a It is possible to run more limited tests (in particular, skip the :ref:`wrappers ` module). See ``egglib-test --help`` for more details.