Download the source code (amaranth-{version}.tar.gz) of Amaranth from Releases.
# For example, to download v0.1.0 source code
wget https://github.com/Shao-Group/amaranth/releases/latest/download/amaranth-0.1.0.tar.gz
tar -zxf amaranth-0.1.0.tar.gz
cd amaranth-0.1.0Amaranth is implemented in C++. A compiler that supports C++20 is needed.
Amaranth 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 Amaranth.
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 Amaranth.
The entire installation typically takes a few minutes to complete.
If Boost has not been downloaded/installed, download Boost (license) from (http://www.boost.org). Uncompress it somewhere (compiling and installing are not necessary).
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
Use the following to compile:
./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 amaranth will appear at src/amaranth.
You can test whether amaranth is correctly installed by printing the help message:
./src/amaranth --help