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.. _getting_started:
Getting Started
===============
.. _getting_started-requirements:
Requirements
------------
These components will almost certainly already be on your system.
* `gcc`_ (4.8+) OR `clang`_ (v3.1+)
* pthreads
* zlib
Double-check your compiler version, to be sure it is compatible.
.. code-block:: console
$ g++ -v
$ clang -v
Additional requirements:
* `Boost`_ (1.55+)
* `Meson`_ (0.48+)
* `Google Test`_
* `htslib`_ (1.4+)
For building API documentation locally:
* `Doxygen`_
For maximal convenience, install htslib and google test in the same parent directory you plan to install pbbam.
.. _Boost: http://www.boost.org/
.. _clang: http://clang.llvm.org/
.. _Meson: https://mesonbuild.com
.. _Ninja: https://ninja-build.org/ (only required when using Meson, optional for CMake)
.. _Doxygen: http://www.stack.nl/~dimitri/doxygen/
.. _gcc: https://gcc.gnu.org/
.. _Google Test: https://github.com/google/googletest
.. _htslib: https://github.com/samtools/htslib.git
.. _getting_started-build:
Clone & Build
-------------
.. note::
The following steps are for building the C++ library and command-line utilities.
The basic steps for obtaining pbbam and building it from source are as follows:
Build and install htslib, per the project's instructions (or on OSX "brew install htslib").
Clone
^^^^^
You should first clone the repository:
.. code-block:: console
$ git clone https://github.com/PacificBiosciences/pbbam.git
$ cd pbbam
Building with Meson
^^^^^^^^^^^^^^^^^^^
Building with Meson is generally faster and more versatile. Meson strictly requires building out of source:
.. code-block:: console
$ mkdir build
$ cd build
$ meson --prefix /my/install/prefix -Dtests=true ..
$ ninja
where ninja will by default utilize a number of threads for compilation equal to the number of logical
cores on your system. Here ``-Dtests=true`` enables pulling in dependencies for testing. In
order to run the test suite, run:
.. code-block:: console
$ ninja test
If you wish to install pbbam, run:
.. code-block:: console
$ ninja install
and ninja will install pbbam to ``/my/install/prefix``.
Integrate
---------
If you built and installed pbbam, pkg-config files will be available to be consumed by projects
wishing to utilize pbbam. Autoconf, CMake, Waf, SCons and Meson all have means to determine
dependency information from pkg-config files.
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