Required libraries

Required libraries

Required libraries

GLIMPSE2 requires several libraries installed on the system:

HTSlib version >= 1.7: A C library for reading/writing high-throughput sequencing data.
Boost version >= 1.65: A set of peer-reviewed portable C++ source libraries. GLIMPSE2 uses three specific Boost libraries: iostreams, program_options and serialization.
SIMDe (bundled): The SIMDe header-only library is included as a git submodule and provides portable SIMD support across x86_64 and ARM64 platforms.

macOS (Homebrew)

On macOS with Homebrew, all required libraries can be installed with a single command:

brew install htslib boost libdeflate

Linux (package manager)

Most Linux distributions package all required libraries. Installing from your distribution’s package manager is the easiest approach.

Debian / Ubuntu

sudo apt-get install build-essential pkg-config \
  libhts-dev libhtscodecs-dev libboost-iostreams-dev libboost-program-options-dev \
  libboost-serialization-dev libdeflate-dev zlib1g-dev libbz2-dev \
  liblzma-dev libssl-dev

Fedora / RHEL / Rocky Linux

sudo dnf install gcc-c++ make pkg-config \
  htslib-devel boost-devel boost-static libdeflate-devel zlib-devel bzip2-devel \
  xz-devel libcurl-devel openssl-devel

Not all Fedora-based distributions (e.g., Amazon Linux) make htslib-devel and libdeflate-devel available in their package repositories. If these packages are not found, you will need to build them from source (see below).

After installing packages, build with make system from the GLIMPSE2 root directory. The build system will automatically locate libraries using pkg-config (for HTSlib) and by searching standard installation paths.

Linux (from source)

If your distribution does not package these libraries, or you need specific versions, you can build them from source.

HTSlib

Building HTSlib is straightforward and does not require root privileges. Please refer to the HTSlib documentation for complete details. Here we provide a basic script to install HTSlib v1.16:

wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2
tar -xf htslib-1.16.tar.bz2
mv htslib-1.16 htslib
cd htslib
autoheader; autoconf; ./configure; #optional
make

After this, you’ll find the libhts.a inside your current directory and the include files inside subdirectory: ./include/

Boost

As GLIMPSE2 only requires few of the Boost libraries, we’ll build the smallest possible Boost build, without requiring root privileges. Please refer to the Boost installation instructions for complete details. Here we provide a basic script to the minimal build of Boost v1.73.0 required to run GLIMPSE2:

wget https://boostorg.jfrog.io/artifactory/main/release/1.73.0/source/boost_1_73_0.tar.bz2
tar --bzip2 -xf boost_1_73_0.tar.bz2
cd boost_1_73_0
./bootstrap.sh --with-libraries=iostreams,program_options,serialization --prefix=../boost #where ../boost is your custom boost installation prefix
./b2 install
cd ../boost #change this to the folder you used as --prefix for the bootstrap script

After this, you will also find a copy of the Boost headers in the include/ subdirectory of the installation prefix (our current directory). The Boost static libraries (libboost_iostreams.a, libboost_program_options.a and libboost_serialization.a) are found in the subfolder ./lib/ of your installation prefix.

Additional libraries

Make sure that the following standard library flags can be used by your compiler on your system:

-lz,-lbz2 and -llzma for reading/writing compressed files.
-lm for basic math operations.
-lpthread for multi-threading
-lcurl for network access.
-lcrypto for cryptographic functions.
-ldeflate for libdeflate compression.

Required libraries

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