Advanced Installation

These steps are valid for a Linux system and tested with Ubuntu 18.04

Update OS

apt-get update
apt_get upgrade -y

Ruby

apt-get install ruby -y

Conda & Python

• Refer to Anaconda website for conda installation
• Create conda environment np3 (it has to be named np3) and install python libraries

conda create -n np3 python=3.6 pandas numpy scipy

OpenMPI

apt-get install build-essential 
cd ${code_path}/packages
tar -zxf openmpi-1.10.2.tar.gz 
cd openmpi-1.10.2 
./configure --prefix=/home/opt/openmpi 
make 
make install

R and R packages

R --slave -e 'install.packages("fastDummies")'
R --slave -e 'install.packages("optparse")'
R --slave -e 'install.packages("doParallel")'
R --slave -e 'install.packages("${code_path}/packages/glmnet_2.0-18.tar.gz", type="source", repos=NULL)'
R --slave -e 'install.packages("e1071")'
R --slave -e 'install.packages("R.oo")'
R --slave -e 'install.packages("BayesTree")'
R --slave -e 'install.packages("stats")'
R --slave -e 'install.packages("matrixStats")'
R --slave -e 'install.packages("Matrix")'
R --slave -e 'install.packages("abind")'
R --slave -e 'install.packages("lars")'
R --slave -e 'install.packages("Rmpi", configure.args=c("--with-Rmpi-include=/home/opt/openmpi/include/", "--with-Rmpi-libpath=/home/opt/openmpi/lib", "--with-Rmpi-type=OPENMPI", "--with-mpi=/home/opt/openmpi"))'
R --slave -e 'install.packages("xgboost")'
R --slave -e 'install.packages("mlr")'
R --slave -e 'install.packages("parallel")'
R --slave -e 'install.packages("parallelMap")'

FIRE and MEME

These packages are for PWM module. If there is no plans for running running PWM network, skip this step.

cd ${code_path}/packages/
unzip -q FIRE-1.1a.zip
cd FIRE-1.1a/
chmod 775 configure
make
chmod +x file.pl

cd ${code_path}/packages/
mkdir -p meme
tar zxf meme-5.1.0.tar.gz
cd meme-5.1.0
./configure --prefix=/home/packages/meme --with-url=http://meme-suite.org/ --enable-build-libxslt
make
make install