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Compile GLIMPSE2

Table of contents

  1. Compile GLIMPSE2

Compile GLIMPSE2

Download the last version of the GLIMPSE2 code using:

git clone

Navigate to the downloaded folder using cd glimpse.

You’ll find there a folder containing all the software packages are other utility folders:

  • chunk: program to define chunks where to run phasing and imputation.
  • common: basic source files used by different tools.
  • concordance: program to verify the accuracy of low-coverage imputation against high-coverage genomes
  • docker: all scripts needed to build a docker file comprising all binaries
  • docs: documentation in html
  • ligate: ligate multiple imputed BCF/VCF files into a single chromosome-length file
  • maps: genetics maps in b37 and b38
  • phase: program to impute and phase low-coverage data.
  • split_reference: prorgram to create GLIMPSE2’s reference file format, used by GLIMPSE2_phase
  • tutorial: test datasets and scripts
  • versions: versioning

Each program in the suite contains the same folder structure:

  • bin: folder for the compiled binary.
  • obj: folder with all binary objects.
  • src: folder with source code.
  • makefile: Makefile to compile the program.

In order to compile a specific tool, for example GLIMPSE2_phase, go in directory of the software (cd phase) and edit the specific makefile at lines so that the following variables are correctly set up (look at the paths already there for an example):

  • HTSSRC: path to the root of the HTSlib library, the prefix for HTSLIB_INC and HTSLIB_LIB paths.
  • HTSLIB_INC: path to the HTSlib header files.
  • HTSLIB_LIB: path to the static HTSlib library (file libhts.a).
  • BOOST_INC: path to the BOOST header files (usually /usr/include).
  • BOOST_LIB_IO: path to the static BOOST iostreams library (file libboost_iostreams.a).
  • BOOST_LIB_PO: path to the static BOOST program_options library (file libboost_program_options.a).
  • BOOST_LIB_SE: path to the static BOOST serialization library (file libboost_serialization.a).

If installed at the system level, static libraries (*.a files) can be located with this command:

locate libboost_program_options.a libboost_iostreams.a libhts.a

Once all paths correctly set up, proceed with the compilation using make. The binary can be found in the bin/ folder of each tool and will have a name similar to GLIMPSE2_phase. You will need to copy the modified makefile in each tool (folder) of GLIMPSE2.