prerequisites.md

Prerequisites

Build sofwares

sudo apt-get install build-essential

Build Python modules

sudo apt-get install python-dev

Perl (>= v5.18.1)

sudo apt-get install perl

• Perl modules:
  Parallel::ForkManager (>= v0.7.5)
  Math::Round (>= v0.06)
  Spreadsheet::WriteExcel (v2.40)

These modules can be installed through CPAN

sudo apt-get install cpan
cpan
nolock_cpan[1]> install Module::Name

R (v3.2.x)

sudo apt-get install r-base r-base-dev

• R packages
  getopt (v1.20.0)
  lsa (v0.73.1)
  ggplot2 (v1.0.1)
  reshape (>= v0.8.5)
  NMF (v0.20.6)
  gplots (>= 2.17.0)
  gtable (>= v0.1.2)
  scales (>= 0.2.5)
  gridExtra (0.9.1)

These packages can be installed in R:

install.packages(https://cran.r-project.org/src/contrib/package_1.1.tar.gz, repos=NULL, type="source")

WebLogo3 (>= v3.3)

sudo pip install weblogo

Annovar (2016Feb01)

The latest release can be downloaded at http://www.openbioinformatics.org/annovar/annovar_download_form.php after free registration.