install: How to install the tool and address the dependencies

In Yves-CHEN/sCNAphase: Esitmate tumor CN profile and tumor cellularity.

Description

sCNAphase is dependent on the NLOPT, which is a C++ library of local and global optimation algorithms. The NLOPT library is expected to be installed beforehand. To locate the header and the library files of NLOPT, the follow two environment variables needs to be set:

export PKG_NLOPT_LIBS="/folder/to/NLOPT/lib"
export PKG_NLOPT_INCLUDE="/folder/to/NLOPT/include"

sCNAphase employs the Boost C++ library for arithmetic calculations. This dependency can be addressed by installing the BH package from CRAN. After these two steps, the following command will install the sCNAphase package.
R CMD INSTALL ./sCNAphase

For faster speed, sCNAphase enables parallel computing using OpenMP, so that it can run on multiple CPUs. This installation procedure has been tested on Linux with GCC-4.4.3.

Note

This compiling procedure was tested on centos, ubuntu with GCC-4.4.3, R-3.0.1.

Yves-CHEN/sCNAphase documentation built on May 10, 2019, 1:54 a.m.