#!/usr/bin/env bash

## Create environment w/ conda ## %%%%%%%%%%%%%%%%%%%%%%%%%%

# Check if environment exists in a conditinonal statement

if [[ -z $(conda env list | grep r_env) ]]; then

  mamba create -y -n r_env r-essentials r-base

fi

mamba activate r_env

## Set up renv ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Rscript -e "

userdir <- unlist(strsplit(Sys.getenv('R_LIBS_USER'),':'))[1L]

repoloc <- 'https://cran.r-project.org/'

install.packages('renv', lib = userdir, repos = repoloc)

"

Rscript -e "renv::init()"

# Install specific packages ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%

# Rscript -e "install.packages('NMF', repos='http://R-Forge.R-project.org')"

Rscript -e "

source('http://renozao.github.io/repotools/install.R')

if (!require('BiocManager', quietly = TRUE))

    install.packages('BiocManager')

BiocManager::install('Biobase')

repotools::install.pkgs('NMF', force=FALSE, quiet=FALSE)

"

# visutils and Seurat is a dependency

Rscript -e "

if (requireNamespace('devtools', quietly = TRUE)) {

  userdir <- unlist(strsplit(Sys.getenv('R_LIBS_USER'),':'))[1L]

  repoloc <- 'https://cran.r-project.org/'

  install.packages('devtools', lib = userdir, repos = repoloc)

}

install.packages("fftwtools")

BiocManager::install("EBImage")

devtools::install_github('iaaka/visutils')

"

# Rscript -e "

# if (requireNamespace('remotes', quietly = TRUE)) {

#   userdir <- unlist(strsplit(Sys.getenv('R_LIBS_USER'),':'))[1L]

#   repoloc <- 'https://cran.r-project.org/'

#   install.packages('remotes', lib = userdir, repos = repoloc)

# }

# remotes::install_github('satijalab/seurat', 'seurat5', quiet = TRUE)

# "