Prerequisites

When building from a source tar ball from the SINA releases page, you will need to install:

• ARB >= 6.0.0
• Boost >= 1.62 - Boost Thread - Boost Program Options - Boost IO Streams - Boost Filesystem - Boost Serialization (SINA < 1.5) - Boost System - Boost Unit Test Framework (when building / running tests)
• TBB >= 2017
• zlib

When building from the raw git source code directly, you will additionally need:

• Autoconf
• Automake
• Libtool
• pkg-config

To build the documentation, you need:

• Sphinx >= 1.8

The easiest way to get all requirements is using Conda:

if test $(uname) == Linux; then
  dist_extra="gcc patchelf coreutils"
else
  dist_extra="llvm"
fi
conda create -n sina_build automake autoconf libtool pkg-config boost arb-bio-devel \
                git tbb tbb-devel glib libiconv bc sed sphinx $dist_extra

Building

1. If you are building from git, start by checking out the source code and generating the configure script:

   git clone https://github.com/epruesse/SINA.git sina
   cd sina
   autoreconf --force --install
   

2. Run the configure script, pointing it at all required libraries as necessary and choosing features and build types:

   ./configure --prefix=install_location \
               --with-arbhome=path_to_arbhome \
               --with-boost=path_to_boost_install \
               --with-boost-libdir=path_to_boost_libs
   

   If you used conda to install your dependencies, this line should work:

   conda activate sina_build
   mkdir build
   cd build
   ../configure --prefix `pwd`/install \
                --disable-docs \
                --with-tbb=$CONDA_PREFIX \
                --with-boost=$CONDA_PREFIX \
                --with-boost-libdir=$CONDA_PREFIX/lib \
                --with-arbhome=$CONDA_PREFIX/lib/arb \
                LDFLAGS="$LDFLAGS -Wl,-rpath,$CONDA_PREFIX/lib"
   

   Essential options to configure:

   ?

   .. program:: configure
   

   ?

   .. option:: --prefix=PATH (/usr/local)
      Set the folder under which ``./bin/sina``, ``./lib/libsina.so`` (or
      ``.dylib``), etc. will be installed.
   

   ?

   .. option:: --with-tbb=PATH
      Set the location of libraries and headers for the Intel
      Threading Building Blocks library.
   

   ?

   .. option:: --with-boost=PATH
      Set the location of the boost header files (without the
      ``include/`` part).
   

   ?

   .. option:: --with-boost-libdir=PATH
      Set the location of the boost lib folder. Often, this is the
      value you used for :option:`--with-boost` with ``/lib``
      appended.
   

   ?

   .. option:: --with-arbhome=PATH
      Set the location of the ARB build directory. Not needed if you
      have ``$ARBHOME`` set to point to the place you built ARB. When
      using the Bioconda package `arb-bio-devel`, use
      `$CONDA_PREFOX/lib/arb` where ``$CONDA_PREFIX`` is the root of
      the environment you installed ARB into.
   

   ?

   .. option:: --with-buildinfo=TEXT
      Set an additional string to be added to the version to identify your build.
   

   ?

   .. option:: --enable-code-coverage
      Add compiler flags to collect code coverage statistics.
   

   ?

   .. option:: --enable-debug
      Enable debug options (sets ``-DDEBUG -O0 -ggdb3`` instead of ``-DNDEBUG -O2 -g``).
   

   ?

   .. option:: --enable-asan
      Enable address sanitizer (sets `-fsanitize=address`).
   

   ?

   .. option:: --enable-fat-tar
      Alters the build so that ``make bindist-gzip`` constructs a fully
      contained tar archive of the build.
   

   ?

   .. option:: --enable-profiling
      Add compiler flags collecting profiling statistics (``-pg``).
   

   ?

   .. option:: --disable-docs
      Do not build the documentation.
   

   If you installed the dependencies in system wide, standard FHS locations, the configure script should detect the locations correctly. Otherwise you may have to use the --with-something options to point it at the right places. If things go wrong, the full error messages will be in config.log.

3. Build SINA (replace <number of cpus with however many cores you've got):

   make -j<number of cpus>
   make install
   

   To build binary archives (see also :option:`--enable-fat-tar`), use:

   ?

   make bindist-gzip2
   

   To run unit tests, call:

   make check
   

   To run only part of the tests, call:

   make check-filtered P=pattern
   

   where pattern matches the name(s) of the test you wish to (re)run.

   To run unit tests collecting code coverage, call:

   make check-code-coverage
   

   To see the full command line of compiler and linker instead of the abbreviated display, append V=1 to the make commandline.