Pysam provides a python interface to the functionality contained
within the htslib C library. There are two ways that these two
can be combined,
The typical installation will be through pypi_:
pip install pysam
This will compile the
builtin htslib source code within pysam.
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
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
libhts.so needs to be known
to the linker once you run pysam, for example by setting the
pysam depends on cython to provide the connectivity to the htslib C
library. The installation of the source tarball (
python 2.7 contains pre-built C-files and cython needs not be present
during installation. However, when installing the source tarball on
python 3 or building from the repository, these pre-built C-files are
not present and cython needs to be installed beforehand.