setup

#!/bin/bash

usage() {
cat <<EOF
================================================================================
setup
================================================================================
Purpose: Sets up the conda and renv environments for the scripts to run.
Also deletes possible unwanted SLURM directives.
Author: Sam Fletcher
Contact: s.o.fletcher@exeter.ac.uk
Dependencies: conda
================================================================================
EOF
    exit 0
}

if [ "$#" -eq 0 ]; then usage; fi 

config_file_location=$1
source "${config_file_location}" || { echo "could not find config file at:
${config_file_location}"; exit 1; }

## =========================== ##
##   REMOVE SLURM DIRECITVES   ##
## =========================== ##

script_list=$(find "${REPO_DIR}" -type f -name "*.sh")

echo "Do you want to remove SLURM directives associated with UoE's HPC?"
echo "(y/n)"
read -r delete_slurm_directives

if [[ "${delete_slurm_directives}" == "y" ]]; then
    for file in $script_list; do
        sed -i "s/#SBATCH -A Research_Project-MRC190311//g" "${file}"
        sed -i "s/#SBATCH -p mrcq//g" "${file}"
    done
fi

## ====================== ##
##   CONDA ENVIRONMENTS   ##
## ====================== ##

source "${CONDA_SHELL}" || { echo "Could not find conda shell at:
${CONDA_SHELL}"; exit 1; }
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels anaconda

conda create --name ChromBinarize-R --file "${REPO_DIR}/requirements-R.txt"
conda create --name ChromBinarize-bedtools --file "${REPO_DIR}/requirements-bedtools.txt"

conda activate ChromBinarize-R

## ==================== ##
##   RENV ENVIRONMENT   ##
## ==================== ##

# Loading an R script whilst in REPO_DIR will automatically download renv
# but only for that R session. The next R session will not have access to 
# renv, resulting in errors. There is no renv environment in RSCRIPT_DIR so
# we execute the install packages function from there to avoid this.
cd "${RSCRIPT_DIR}" || exit 1
Rscript -e "install.packages('renv', repo='https://cloud.r-project.org')"

cd "${REPO_DIR}" || exit 1
Rscript -e "renv::restore(); library(fitdistrplus); print('success')"