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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+)
* `CMake`_ (3.0+)
* `Google Test`_
* `htslib`_ (1.4+)
For additional languages:
* `SWIG`_ (3.0.5+)
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/
.. _CMake: https://cmake.org/
.. _Meson: http://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
.. _SWIG: http://www.swig.org/
.. _getting_started-build:
Clone & Build
-------------
.. note::
The following steps are for building the C++ library and command-line utilities.
If you are integrating pbbam into a C#, Python, or R project, take a look at the
instructions for :ref:`additional languages <swig_bindings>`.
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 CMake
^^^^^^^^^^^^^^^^^^^
When building with CMake, create a separate build directory:
.. code-block:: console
$ mkdir build
$ cd build
$ cmake ..
$ make -j 4 # compiles using 4 threads
Output:
* Library : <pbbam_root>/lib
* Headers : <pbbam_root>/include
* Utilities : <pbbam_root>/bin
You may need to set a few options on the cmake command, to point to dependencies' install locations.
Common installation-related options include:
* GTEST_SRC_DIR
Add these using the '-D' argument, like this:
.. code-block:: console
$ cmake .. -DGTEST_SRC_DIR="path/to/googletest"
To run the test suite, run:
.. code-block:: console
$ make test
To build a local copy of the (Doxygen-style) API documentation, run:
.. code-block:: console
$ make doc
And then open <pbbam_root>/docs/html/index.html in your favorite browser.
.. _getting_started-integrate:
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
---------
CMake-based projects
````````````````````
For CMake-based projects that will "ship with" or otherwise live alongside pbbam, you can
use the approach described here.
Before defining your library or executable, add the following:
.. code-block:: cmake
add_subdirectory(<path/to/pbbam> external/build/pbbam)
When it's time to run "make" this will ensure that pbbam will be built, inside your own project's
build directory. After this point in the CMakeLists.txt file(s), a few variables will be available
that can be used to setup your include paths and library linking targets:
.. code-block:: cmake
include_directories(
${PacBioBAM_INCLUDE_DIRS}
# other includes that your project needs
)
add_executable(foo)
target_link_libraries(foo
${PacBioBAM_LIBRARIES}
# other libs that your project needs
)
Non-CMake projects
``````````````````
If you're using something other than CMake for your project's build system, then you need to point
it to pbbam's include directory & library, as well as those of its dependencies (primarily htslib).
If you built and installed pbbam using Meson, 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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