Required software for hichipper

The following dependencies need to be installed before running hichipper: bedtools, OpenSSL, libcurl, libxml2, and samtools. Depending on if you want some bonus functionality, you may need to download additional requirements.

Except for bedtools, these other dependencies came out of the box with the unix/linux systems that we’ve used hichipper on.

But just to be safe, on an Ubuntu system, all of the dependencies can be installed with:

apt-get install bedtools libssl-dev libcurl4-openssl-dev libxml2-dev

Additionally, R must be available in the environment as well as a reasonably recent version of pandoc and a few packages that can be downloaded running the following in an ‘R’ environment. :

install_pkgs <- function(pkg){
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg)) install.packages(new.pkg, dependencies = TRUE, repos="")
install_pkgs(c("data.table", "devtools", "foreach", "ggplot2", "knitr", "networkD3", "readr", "reshape2"))

install_pkgs_bioc <- function(pkg){
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg)) biocLite(new.pkg, dependencies = TRUE, repos="")

or simply download this R script and run:

Rscript requirementsInstall.R

Convenient pandoc binaries for Linux, Mac and Windows are available for download from RStudio. If you prefer to install pandoc globally on your machine, installation instructions can be found here.