Installation

1. Using R devtools

   install.packages("devtools")
   library(devtools)
   install_github("broadinstitute/ichorCNA", "--no-docs")
   

2. Manual installation
   a. Checkout the latest release of ichorCNA from GitHub

   git clone git@github.com:broadinstitute/ichorCNA.git  
   

   b. Install R dependencies (in R)

   ## install from CRAN
   install.packages("plyr") # version > 1.8.4
   ## install packages from
   source("https://bioconductor.org/biocLite.R")
   biocLite("HMMcopy") # version >= 1.14.0
   biocLite("GenomeInfoDb") # version >= 1.8.7
   

   c. Install the ichorCNA R package

   ## from the command line and in the directory where ichorCNA github was cloned.
   R CMD INSTALL ichorCNA  
   

3. Other dependencies
   a. Install the HMMcopy suite from http://compbio.bccrc.ca/software/hmmcopy/
   Please follow instructions on the HMMcopy website.