install_melonpann.sh

( conda create -y -n "melonpann" && source activate "melonpann" && \
  conda install r-base=3.5.0 r-devtools r-fbasics -yc r && \
  R -q -e "install.packages('BiocManager', repos='http://cran.r-project.org'); \
           library('BiocManager'); BiocManager::install('ccrepe');" && \
  R -q -e "install.packages('optparse', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('AssocTests', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('glmnet', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('HDtweedie', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('getopt', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('doParallel', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('vegan', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('data.table', repos='http://cran.r-project.org')" && \
  cran="https://cran.r-project.org/src/contrib/Archive" && \
  R -q -e "library('devtools'); devtools::install_url('${cran}/DatABEL/DatABEL_0.9-6.tar.gz')" && \
  R -q -e "library('devtools'); devtools::install_url('${cran}/GenABEL.data/GenABEL.data_1.0.0.tar.gz')" && \
  R -q -e "library('devtools'); devtools::install_url('${cran}/GenABEL/GenABEL_1.8-0.tar.gz')" && \
  git clone https://github.com/biobakery/melonnpan.git && R CMD INSTALL melonnpan && rm -rf melonnpan && \
  conda deactivate ) || { echo "ERROR: Conda melonpann install failed"; exit 1; }