Installing and running HiC-Pro

Installing HiC-Pro

Installing dependency packages

bowtie2

$ spack install bowtie2 %gcc@5.4.0

samtools

$ spack install samtools %gcc@5.4.0

Python 2.7 with numpy, scipy, pysam and bx-python

$ spack install py-numpy+blas+lapack %gcc@5.4.0 ^openmp threads=openmp
$ spack install py-scipy %gcc@5.4.0 ^openblas threads=openmp
$ spack install py-pysam %gcc@5.4.0
$ spack spec py-bx-python %gcc@5.4.0 ^py-numpy+blas+lapack^openblas threads=openmp

R with RColorBrewer and Ggplot2 packages

Follow instructions on https://pi.sjtu.edu.cn/doc/R .

$ spack install r-rcolorbrewer %gcc@5.4.0 ^r+external-lapack^openblas threads=openmp
$ spack install r-ggplot2 %gcc@5.4.0 ^r+external-lapack^openblas threads=openmp

Building HiC-Pro

Reference