magic-r-environment-maker.sh

#!/bin/bash

CONDA_DOWNLOAD_LOCATION=$BUILD_DIR/miniconda.sh
CONDA_INSTALL_LOCATION=$BUILD_DIR/miniconda

if [ ! -f $CONDA_DOWNLOAD_LOCATION ]; then
  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $CONDA_DOWNLOAD_LOCATION
fi

bash $CONDA_DOWNLOAD_LOCATION -b -p $CONDA_INSTALL_LOCATION

i r
export PATH=$CONDA_INSTALL_LOCATION/bin:$PATH

echo "Using default condarc"
echo "always_yes: True
channels:
- conda-forge
- bioconda
- r
- defaults
" > $BUILD_DIR/contarc
export CONDARC=$BUILD_DIR/condarc

conda env remove r_env

conda create -n r_env -c r r bioconductor-rgraphviz bioconductor-rbgl gcc

source activate r_env

conda update --all

Rscript init.r