#!/bin/bash
set -e  # Stop on error

SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)

CONDA_ENV_PY3=encode-chip-seq-pipeline
CONDA_ENV_PY2=encode-chip-seq-pipeline-python2
REQ_TXT_PY3=${SH_SCRIPT_DIR}/requirements.txt
REQ_TXT_PY2=${SH_SCRIPT_DIR}/requirements_py2.txt
SRC_DIR=${SH_SCRIPT_DIR}/../src

conda --version  # check if conda exists

echo "=== Installing pipeline's Conda environments ==="
conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -c defaults -c r -c bioconda -c conda-forge
conda create -n ${CONDA_ENV_PY2} --file ${REQ_TXT_PY2} -y -c defaults -c r -c bioconda -c conda-forge

echo "=== Configuring for pipeline's Conda environments ==="
CONDA_PREFIX_PY3=$(conda env list | grep -E "\b${CONDA_ENV_PY3}[[:space:]]" | awk '{if (NF==3) print $3; else print $2}')
CONDA_PREFIX_PY2=$(conda env list | grep -E "\b${CONDA_ENV_PY2}[[:space:]]" | awk '{if (NF==3) print $3; else print $2}')

if [ ! "${CONDA_PREFIX_PY3}" -o ! "${CONDA_PREFIX_PY2}" ];
then
	echo "Error: Pipeline's Conda environments not found."
	echo "Try to reinstall pipeline's Conda environments."
	echo
	echo "1) $ bash uninstall_conda_env.sh"
	echo "2) $ bash install_conda_env.sh"
	exit 1
fi

# make activate.d to init pipeline's Conda envs
CONDA_LIB="${CONDA_PREFIX_PY3}/lib"
CONDA_BIN="${CONDA_PREFIX_PY3}/bin"
CONDA_ACTIVATE_D="${CONDA_PREFIX_PY3}/etc/conda/activate.d"
CONDA_DEACTIVATE_D="${CONDA_PREFIX_PY3}/etc/conda/deactivate.d"
CONDA_ACTIVATE_SH="${CONDA_ACTIVATE_D}/env_vars.sh"
CONDA_DEACTIVATE_SH="${CONDA_DEACTIVATE_D}/env_vars.sh"
mkdir -p ${CONDA_ACTIVATE_D}
mkdir -p ${CONDA_DEACTIVATE_D}
touch ${CONDA_ACTIVATE_SH}
touch ${CONDA_DEACTIVATE_SH}

# disable multithreading for BLAS
echo "export OPENBLAS_NUM_THREADS=1" > ${CONDA_ACTIVATE_SH}
echo "export MKL_NUM_THREADS=1" >> ${CONDA_ACTIVATE_SH}
echo "unset OPENBLAS_NUM_THREADS MKL_NUM_THREADS" >> ${CONDA_DEACTIVATE_SH}

# to prevent conflict between Conda's python packages and user's local one
echo "export PYTHONNOUSERSITE=True" >> ${CONDA_ACTIVATE_SH}
echo "unset PYTHONNOUSERSITE" >> ${CONDA_DEACTIVATE_SH}

# LD_LIBRARY_PATH due to libgcc problem
echo "export OLD_LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}" >> ${CONDA_ACTIVATE_SH}
echo "export LD_LIBRARY_PATH=${CONDA_LIB}:\${LD_LIBRARY_PATH}" >> ${CONDA_ACTIVATE_SH}

echo "export LD_LIBRARY_PATH=\${OLD_LD_LIBRARY_PATH}" >> ${CONDA_DEACTIVATE_SH}
echo "unset OLD_LD_LIBRARY_PATH" >> ${CONDA_DEACTIVATE_SH}

# to prevent conflict between Conda's R and global(local) R
echo "export OLD_R_HOME=\${R_HOME}" >> ${CONDA_ACTIVATE_SH}
echo "export OLD_R_LIBS=\${R_LIBS}" >> ${CONDA_ACTIVATE_SH}
echo "export R_HOME=${CONDA_LIB}/R" >> ${CONDA_ACTIVATE_SH}
echo "export R_LIBS=${CONDA_LIB}/R/library" >> ${CONDA_ACTIVATE_SH}

echo "export R_HOME=\${OLD_R_HOME}" >> ${CONDA_DEACTIVATE_SH}
echo "export R_LIBS=\${OLD_R_LIBS}" >> ${CONDA_DEACTIVATE_SH}
echo "unset OLD_R_HOME" >> ${CONDA_DEACTIVATE_SH}
echo "unset OLD_R_LIBS" >> ${CONDA_DEACTIVATE_SH}

# hack around the need for both python2 and python3 in the same environment
cd ${CONDA_BIN}
ln -s ../../${CONDA_ENV_PY2}/bin/python2

echo "=== Updating pipeline's Conda environments ==="
cd ${CONDA_BIN}
chmod u+rx ${SRC_DIR}/*.py
# copy all python scripts in /src into conda env bin dir
cp -f ${SRC_DIR}/*.py ${CONDA_BIN}/
chmod u+rx ${CONDA_BIN}/encode_*.py

echo "=== All done successfully ==="