haplotyping with SDhaP

I need to use sdhap program but it is not easy to install. It has some dependencies. LAPACK (Linear Algebra PACKage) is written in Fortran. There are some LAPACK APIs for C. SDhaP needs the c-LAPACK version of ATLAS (Automatically Tuned Linear Algebra Software). ATLAS also contains some others libraries. So installing ATLAS with the option (--with-netlib-lapack-tarfile) is enough. And it's not needed to install clapack or cblas or lapack seperately!

ATLAS

You first need to build ATLAS (Automatically Tuned Linear Algebra Software) libraries and also need lapack using following instruction.

Download

wget https://netix.dl.sourceforge.net/project/math-atlas/Stable/3.10.3/atlas3.10.3.tar.bz2

tar xjf atlas3.10.3.tar.bz2
mv ATLAS ATLAS_source


mkdir lapack_source; cd lapack_source
wget http://www.netlib.org/lapack/lapack-3.8.0.tar.gz 

cd ..
mkdir ATLAS_out; mkdir ATLAS_out/lib; mkdir ATLAS_out/include;
mkdir ATLAS_build
cd ATLAS_build

Configuration

In the ATLAS_source folder, there is pdf file as the installation guid. Step 3 The ATLAS configure is very important. You may also use

${PATH}='/mnt/scratch/majid001/sdhap_full_inst/'

${PATH}/ATLAS_source/configure --help

You need to check your architecture and your cpu and type it as Mhz in option DPentiumCPS.

cat /proc/cpuinfo 
uname -m

for x86 use -DPentiumCPS=2300 and for non x86 use -D c -DWALL. Default option generates static library. You can add --shared to generate also shared library.

For generic libraries

${PATH}/ATLAS_source/configure --prefix=${PATH}/ATLAS_out --with-netlib-lapack-tarfile=${PATH}/lapack_source/lapack-3.8.0.tar.gz  -b 64 -V -1 -A x86x87 -t 2 -v 2

For your case

${PATH}/ATLAS_source/configure --prefix=${PATH}/ATLAS_out --with-netlib-lapack-tarfile=${PATH}/lapack_source/lapack-3.8.0.tar.gz  -b 64 -D c -DPentiumCPS=2300  -v 2

It takes several minutes.

build

make 

It may takes few days!

make check    
make ptcheck  
make time  
make install

SDhaP

build

The official line by author

gcc SDhaP_poly.c -o hap -L/usr/lib64/atlas -llapack -lcblas -I/usr/include/atlas

I'm using the followings for my mac and WUR fisher server.

gcc SDhaP_poly.c -g -o out -L/ATLAS_build/lib -lcblas -llapack  -I/ATLAS_out/include -lm -latlas -lf77refblas -L/usr/local/Cellar/gcc/8.3.0_2/lib/gcc/8/ -lgfortran

gcc SDhaP_poly.c -g -o hap_polya -I/usr/include/x86_64-linux-gnu/ -llapack -lcblas -lm

Run

k=3

./hap_poly fragment_file out.hap $k

References

"SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming", Shreepriya Das* and Haris Vikalo