Setup Guide for Day 4

Note: This setup guide is designed for Linux systems, particularly Ubuntu. For Windows users, please use WSL2 or a Linux virtual machine.

0. Install required software

   sudo apt update
   sudo apt install -y bcftools build-essential

1. Install HDF5

   • Download the HDF5 source package here.

2. Extract the Source Code

   • Extract the source from the hdf5-1.8.23.tar.gz file

     tar -xzvf hdf5-1.8.23.tar.gz

   • Navigate to the extracted directory

     cd hdf5-1.8.23

3. Build and Install HDF5

   • Use the following commands to configure, build, and install HDF5

     ./configure

     make

     make install

4. Compile Roven’s Program

   • Download Roven’s script here

   • Create a file named build.sh and add the following content:

         #!/bin/bash
     
         main=hdf5-1.8.23/src
         lib=/home/riza/Tools/hdf5-1.8.23/hdf5/lib  # Change this path to where HDF5 was installed
         include=$main
         PATH="$main/bin:$PATH"
         export LD_RUN_PATH=$lib
         export LDFLAGS="-L$lib"
         export CPPFLAGS="-I$include"
         header=$include
     
         g++ -o loadmatrix_geno -I $header loadmatrix_SNP-annot.cpp -lhdf5 -L$lib

     Important: Change the path assigned to the lib variable to match the directory where you installed the HDF5 library on your system

   • Make build.sh executable

     chmod u+x build.sh

   • Run the script

     ./build.sh

   • Verify. Run the compiled program:

     ./loadmatrix_geno

     • You should see the following:

        ./loadmatrix_geno
        -r  Number of rows in the input genotype matrix
        -m chunk dimension (height)
        -n chunk dimernsion (width)
        -t transposed orientation
        -o output-file
        ERROR: Cannot open file.