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INSTALL.md

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Install

For running the latest 'Nucleosome Dynamics CLI' version, simply clone the master branch of the present repository. It contains the R scripts in /bin and /statistics folders.

git clone https://github.com/nucleosome-dynamics/nucleosome_dynamics.git

Some functionalities of these scripts depend on third-party software that needs an independent installation:

  • nucleR R package
  • NucDyn R package
  • UCSC wig utils

1. nucleR R package

Nucleosome positioning predictions in 'Nucleosome Dynamics CLI' relies on the specific methods implemented in 'nucleR' package. There are several options for installing nucleR. Check them all here.

2. NucDyn R package

Nucleosome architecture comparison in 'Nucleosome Dynamics CLI' depend on the specific methods implemented in 'NucDyn' package. There are also several options for installing NuclDyn. Check them all here.

3. UCSC wig utils

WIG format conversions (wig, bigwig) in 'Nucleosome Dynamics CLI' relies on the stand-alone binaries maintainced by UCSC. For installing them, download the executables of interest (wigToBigWig, bigWigToWig and fetchChromSizes) for your operating system from the official binary repository. For a Linux 64-bit machine do:

mkdir wig_utils;
cd wig_utils;
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig &&  \ 
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig  && \ 
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes;
chmod a+x *

Make sure you save them in a directory included in your $PATH, or simply add your installation path directory to it by editing in your .bashrc home directory the following line:

export PATH="$PATH:/absolute/path/to/wig_utils"

And source it:

source .bashrc