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Changes for Summit at CU Research Computing.

I have modified the configure file to work on summit.

  • Its 'grep/sed' command for determining the version of the boost library was failing because of a leading space present in the version.h file.

Installation in R.

As of Thu Jan 25 11:08:56 MST 2018

the following modules must be loaded.

ml is a shortcut for module load.

  • ml intel

  • ml impi

  • ml boost

  • ml R

Locally installing in R

A local install path must be set inside R. For us, your project space is encouraged, and I recommend creating an R directory:

mkdir /projects/username@colostate.edu/R

$ R
.libPaths('/projects/username@colostate.edu/R)

The original repository uses devtools, but that may be insufficient to install dependencies on Summit. To try it, update the url in that command.

require(devtools)
devtools::install_github('meekrob/spp', build_vignettes = FALSE)

Preferably, download this package using git clone and the url of this repository, it should create a directory called spp. In the same directory, start R, and do

.libPaths('/projects/username@colostate.edu/R') # Set your local install path
install.packages("spp", repos=NULL) # Should install dependancies

This will also compile SPP, and may take a while.

To run SPP

In R:

.libPaths('/projects/username@colostate.edu/R') # Set your local install path
require(spp)

If the require succeeds without reporting errors, the installation worked.

Original README

ChIP-seq processing pipeline

An R package for anlaysis of ChIP-seq and other functional sequencing data. Please see package homepage for details.

Requirements

A unix-flavored OS with R and Boost C++ installed.

Installation

You can use modtools to install SPP:

require(devtools)
devtools::install_github('hms-dbmi/spp', build_vignettes = FALSE)

Alternatively, download a .tar.gz containing the latest release and use the standard R installation command, e.g.:

R CMD INSTALL spp_1.13.tar.gz

Note: if Boost libraries are installed in a non-standard location, please specify the location in a BOOST_ROOT environment variable prior to running the installation.

export BOOST_ROOT=/path/boost_1_58_0/