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 wrappers module, the corresponding program must be found in your system and EggLib should be configured accordingly (see Configuring 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 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 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 VCF is never included. With variable HTSLIB=1, the 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 VCF is masked and the class is silently skipped. So HTSLIB=1 is recommended if 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

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 https://pypi.org/project/EggLib/#files. Older releases are also archived there.

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 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 wrappers module, either permanently or temporarily. For details, see Configuring 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 io.VCF class) are available:

$ egglib-test -a

It is possible to run more limited tests (in particular, skip the wrappers module). See egglib-test --help for more details.