==== description ====
[[https://odelaneau.github.io/GLIMPSE/|GLIMPSE2]] is a set of tools for low-coverage whole genome sequencing imputation. GLIMPSE2 is based on the GLIMPSE model and designed for reference panels containing hundreads of thousands of reference samples, with a special focus on rare variants. 
  * **GLIMPSE2_chunk** splits the genome into chunks for imputation and phasing
  * **GLIMPSE2_split_reference** creates the reference panel representation used by GLIMPSE2_phase. It allows major speedups for large reference panels.
  * **GLIMPSE2_phase** program to impute and phase low coverage sequencing data
  * **GLIMPSE2_ligate** concatenates phased chunks of data into chromosome-wide phased files
=== citation ===
If you use GLIMPSE in your research work, please cite the following papers [[https://odelaneau.github.io/GLIMPSE/|more]].

==== software version ====
Bellow description covers preparation and compilation of GLIMPSE2_phase v2.0.0 ((Software is available as static binaries, see https://odelaneau.github.io/GLIMPSE/docs/installation/static_binaries))


==== prepare software ====
Login to anthill23, and download required sources ((this will take 8 minutes))
  mkdir -p ~/anthill23_soft/glimpse
  
  cd ~/anthill23_soft/glimpse
  git clone https://github.com/samtools/htslib htslib_src
  cd htslib_src
  git submodule update --init --recursive
  
  cd ~/anthill23_soft/glimpse
  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 ~/anthill23_soft/glimpse
  git clone https://github.com/odelaneau/glimpse.git


start interactive session in which download and compile htslib, boost, glimpse2_phase ((this will take 20 minutes)):

  @anthill23:~$ srun --cpus-per-task 8 --mem-per-cpu 20G  -J glimpse_prep --partition=medium --pty --preserve-env bash
  

compile htslib ((this will take 6 minutes)):
  cd ~/anthill23_soft/glimpse/htslib_src
  autoreconf -i
  ./configure --enable-libcurl --prefix=/home/users/${USER}/anthill23_soft/glimpse/htslib
  make
  make install
  
  
compile boost ((this will take 1 minute)): 
  cd ~/anthill23_soft/glimpse/boost_1_73_0
  ./bootstrap.sh --with-libraries=iostreams,program_options,serialization --prefix=../boost
  ./b2 install
  
compile GLIMPSE2_phase ((this will take 3 minutes)): 
  cd ~/anthill23_soft/glimpse/glimpse/phase
  sed -i 's/desktop: HTSSRC.*/desktop: HTSSRC=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/htslib/' makefile
  sed -i 's/desktop: HTSLIB_INC.*/desktop: HTSLIB_INC=\$(HTSSRC)\/include/' makefile
  sed -i 's/desktop: HTSLIB_LIB.*/desktop: HTSLIB_LIB=\$(HTSSRC)\/lib\/libhts.a/' makefile
  sed -i 's/desktop: BOOST_INC.*/desktop: BOOST_INC=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/include/' makefile
  sed -i 's/desktop: BOOST_LIB_IO.*/desktop: BOOST_LIB_IO=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_iostreams.a/' makefile
  sed -i 's/desktop: BOOST_LIB_PO.*/desktop: BOOST_LIB_PO=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_program_options.a/' makefile
  sed -i 's/desktop: BOOST_LIB_SE.*/desktop: BOOST_LIB_SE=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_serialization.a/' makefile
  make desktop
  
compile GLIMPSE2_chunk / ligate / split_reference 
  #repeat the same as for GLIMPSE2_phase described above, but in different folder
  cd ~/anthill23_soft/glimpse/glimpse/chunk           # for GLIMPSE2_chunk
  cd ~/anthill23_soft/glimpse/glimpse/ligate          # for GLIMPSE2_ligate
  cd ~/anthill23_soft/glimpse/glimpse/split_reference # for GLIMPSE2_split_reference
 
test created binary, you should get similar output :
  cd ~/anthill23_soft/glimpse/glimpse/phase
  ./bin/GLIMPSE2_phase 
  
  [GLIMPSE2] Phase and impute low coverage sequencing data
    * Authors              : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
    * Contact              : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch
    * Version              : GLIMPSE2_phase v2.0.0 / commit = 0fcf590 / release = 2023-10-09
    * Citation             : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213
    *                      : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0
    * Run date             : 05/11/2023 - 08:17:29
  
  ERROR: You must specify input files using one of the following options: --bam, --bam-list or --input-gl

finish
  #exit interactive mode when finished with exit command
  exit


==== sbatch example ====
...FIXME

==== performance tests ====
... FIXME