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INSTALL.md

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Install TERRACE from Source

Download the source code of latest TERRACE from here. TERRACE uses additional libraries of Boost and htslib. If they have not been installed in your system, you first need to download and install them. You might also need to export the runtime library path to certain environmental variable (for example, LD_LIBRARY_PATH, for most linux distributions). After install these dependencies, you then compile the source code of TERRACE. If some of the above dependencies are not installed to the default system directories (for example, /usr/local, for most linux distributions), their corresponding installing paths should be specified to configure of TERRACE. The entire installation typically takes a few minutes to complete.

Download Boost

If Boost has not been downloaded/installed, download Boost (license) from (http://www.boost.org). Uncompress it somewhere (compiling and installing are not necessary).

Install htslib

If htslib has not been installed, download htslib (license) from (http://www.htslib.org/) with version 1.5 or higher. Note that htslib relies on zlib. So if zlib has not been installed in your system, you need to install zlib first. To do so, download zlib (license) at (https://zlib.net/). Use the following commands to install zlib:

./configure
make
make install

After installing zlib, use the following commands to build htslib:

./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no
make
make install

The default installation location of htslib is /usr/lib. If you would install it to a different location, replace the above configure line with the following (by adding --prefix=/path/to/your/htslib to the end):

./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no --prefix=/path/to/your/htslib

In this case, you also need to export the runtime library path (note that there is an additional lib following the installation path):

export LD_LIBRARY_PATH=/path/to/your/htslib/lib:$LD_LIBRARY_PATH

Build TERRACE

Use the following to compile TERRACE:

./configure --with-htslib=/path/to/your/htslib --with-boost=/path/to/your/boost
make

If some of the dependencies are installed in the default system directory (for example, /usr/lib), then the corresponding --with- option might not be necessary. The executable file terrace will appear at src/terrace.