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Installing pysam

Pysam can be installed through conda_, pypi_ and from the repository. The recommended way to install pysam is through conda/bioconda.

Conda installation

To install pysam in your current conda_ environment, type:

conda config --add channels r
conda config --add channels bioconda
conda install pysam

This will install pysam from the bioconda_ channel and automatically makes sure that dependencies are installed. Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X.

Pypi installation

Pysam provides a python interface to the functionality contained within the htslib_ C library. There are two ways that these two can be combined, builtin and external.

Builtin

The typical installation will be through pypi_:

pip install pysam

This will compile the builtin htslib source code within pysam.

htslib_ can be configured at compilation to turn on additional features such support using encrypted configurations, enable plugins, and more. See the htslib_ project for more information on these.

Pysam will attempt to configure htslib_ to turn on some advanced features. If these fail, for example due to missing library dependencies (libcurl, libcrypto), it will fall back to conservative defaults.

Options can be passed to the configure script explicitely by setting the environment variable HTSLIB_CONFIGURE_OPTIONS. For example:

export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
pip install pysam

External

pysam can be combined with an externally installed htslib_ library. This is a good way to avoid duplication of libraries. To link against an externally installed library, set the environment variables HTSLIB_LIBRARY_DIR and HTSLIB_INCLUDE_DIR before installing:

export HTSLIB_LIBRARY_DIR=/usr/local/lib
export HTSLIB_INCLUDE_DIR=/usr/local/include
pip install pysam

Note that the location of the file :file:`libhts.so` needs to be known to the linker once you run pysam, for example by setting the environment-varirable LD_LIBRARY_PATH.

Note that generally the pysam and htslib version need to be compatible. See the release notes for more information.

Installation from repository

pysam depends on cython_ to provide the connectivity to the htslib_ C library. The installation of the source tarball (:file:`.tar.gz`) contains pre-built C-files and cython needs not be present during installation. However, when installing from the repository, cython needs to be installed beforehand.

To install from repository, type:

python setup.py install

For compilation options, see the section on Pypi installation above.

Requirements

Depending on the installation method, requirements for building pysam differ.

When installing through conda_, dependencies will be resolved by the package manager. The pip_ installation and installation from source require a C compiler and its standard libraries as well as all requirements for building htslib. Htslib requirements are listed in the htslib/INSTALL file.

Installing from the repository will require cython_ to be installed.