GLIMPSE2 requires several libraries installed on the system. Here we assume most of the libraries are available, and we focus on two main libraries:
- 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:
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:
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_serialization.a) are found in the subfolder
./lib/ of your installation prefix.
Make sure that the following standard library flags can be used by g++ on your system:
-llzmafor reading/writing compressed files.
-lmfor basic math operations.
You can do so by checking the outcome of the following commands:
locate -b '\libz.so' locate -b '\libbz2.so' locate -b '\liblzma.so' locate -b '\libm.so' locate -b '\libpthread.so' locate -b '\libcurl.so'