get_wochenende.sh

# Dr Colin Davenport
# June - Aug 2021
# A helper script to copy Wochenende scripts/directory to the current path.
# Uses settings from the config yaml file

echo "INFO: setup.sh should have created  WOCHENENDE_DIR environment variable on this server and user account"
echo "INFO: WOCHENENDE_DIR detected as: " $WOCHENENDE_DIR

# check if env variables are correctly defined.
if [[ -z "${WOCHENENDE_DIR}" || -z "${HAYBALER_DIR}" ]]; then
    echo "ERROR: WOCHENENDE_DIR or HAYBALER_DIR was not found. Use setup.sh in the Wochenende project to set the directory properly. Exiting! "
    exit 1
fi

#path_we=/mnt/ngsnfs/tools/dev/Wochenende
#path_we=/mnt/ngsnfs/tools/dev/we_config2/wochenende
path_we=$WOCHENENDE_DIR

cp $path_we/README* .
cp $path_we/*.sh .
cp $path_we/*.py .
cp -R $path_we/extract/ .
cp -R $path_we/plots/ .
cp -R $path_we/reporting/ .
cp -R $path_we/growth_rate/ .
cp -R $path_we/raspir/ .
cp -R $path_we/metaG/ .

echo "INFO: If you get errors here check setup.sh was configured and run properly"
echo "INFO: Completed get_wochenende.sh"
echo ""