install.sh

#!/usr/bin/env bash
appEnvName="RNAsequest"
appEnvPath="~/.conda/env/$appEnvName"

condaPath=$(which conda)
if [[ ${#condaPath} -lt 3 ]]; then
    echo "Missing conda"
    echo "Please install conda and add it into PATH"
    exit
else
    echo "conda in $condaPath"
fi

src="$(dirname $0)/src"
condaPath=$(dirname $(dirname $condaPath))
if { conda env list | grep "^$appEnvPath"; } >/dev/null 2>/dev/null; then conda env remove -n $appEnvName; fi
#conda env create -f install.yml
# mamba is not in the base conda
conda create -y -p $appEnvPath -c conda-forge r-base=4.3.3 python=3.10 mamba
source $condaPath/etc/profile.d/conda.sh
conda activate $appEnvPath
cat install.yml > install_local.yml
echo "  PKG_CONFIG_PATH: $appEnvPath/lib/pkgconfig" >> install_local.yml
mamba env update -f install_local.yml

echo "export condaEnv='. $condaPath/etc/profile.d/conda.sh;conda activate $appEnvPath'" > $src/.env
echo "export PATH=$PATH" >> $src/.env
echo "export SGE_EXECD_PORT=$SGE_EXECD_PORT" >> $src/.env
echo "export SGE_QMASTER_PORT=$SGE_QMASTER_PORT" >> $src/.env
echo "export SGE_ROOT=$SGE_ROOT" >> $src/.env
echo "export SLURM_CONF=$SLURM_CONF" >> $src/.env
conda deactivate

## additional packages which are not available on anaconda
env -i src="$src" bash -c 'source $src/.env;eval $condaEnv;R -q -e '"'"'suppressWarnings({if(!require(revealjs)) install.packages("revealjs",repos = "https://cloud.r-project.org/")})'"'"

echo "If no errors above, RNAsequest installation/configuration is successful!"