entrypoint.sh

#!/bin/bash
sed -i s/localhost/$HOSTNAME/g /etc/slurm/slurm.conf
/etc/init.d/postfix start
/etc/init.d/cron start
chown 106 /etc/munge/munge.key
/etc/init.d/munge start
/etc/init.d/slurmctld start
/etc/init.d/slurmd start
#/etc/init.d/postgres start

chown root /etc/crontab # in case it was mounted from local dir

if [ "${MODE}" = 'TESTING' ]; then
    exec perl t/test_fixture.pl --carpalways -v "${@}"
fi

umask 002

# load empty fixture and run any missing patches

echo "CHECKING IF A DATABASE NEEDS TO BE INSTALLED...";

if [[ $(psql -lqt -h ${PGHOST} -U ${PGUSER}  | cut -d '|' -f1  | sed 's/^[[:blank:]]*//;s/[[:blank:]]*$//;' |  grep -w breedbase ) = '' ]]; then
    echo "INSTALLING DATABASE...";
    echo "CREATING web_usr...";
    psql -d postgres -c "CREATE USER web_usr PASSWORD 'postgres';"
    echo "CREATING breedbase DATABASE...";
    
    psql -d postgres -c "CREATE DATABASE breedbase; "
    if [ -e '/db_dumps/empty_breedbase.sql' ]
    then
	echo "LOADING empty_breedbase dump...";
	psql -f /db_dumps/empty_breedbase.sql
	(cd db && ./run_all_patches.pl -u ${PGUSER} -p ${PGPASSWORD} -h ${PGHOST} -d ${PGDATABASE} -e admin )
    else
	echo "LOADING cxgn_fixture.sql dump...";
	psql -f t/data/fixture/cxgn_fixture.sql
	(cd db && ./run_all_patches.pl -u ${PGUSER} -p ${PGPASSWORD} -h ${PGHOST} -d ${PGDATABASE} -e janedoe )
    fi
    
    
fi

# create necessary dirs/permissions if we have a docker volume dir
# at /home/production/volume

if [[ -e /home/production/volume ]]
then
    if [[ ! -e /home/production/volume/archive ]]
    then
        mkdir /home/production/volume/archive
        chown www-data /home/production/volume/archive
	chmod 770 /home/production/volume/archive
    fi

    if [[ ! -e /home/production/volume/logs ]]
    then
        mkdir /home/production/volume/logs
        chown www-data /home/production/volume/logs
	chmod 770 /home/production/volume/logs
    fi

    if [[ ! -e /home/production/volume/blast ]]
    then
        mkdir /home/production/volume/blast
    fi

    if [[ ! -e /home/production/volume/public ]]
    then
        mkdir /home/production/volume/public
	chown www-data /home/production/volume/public
	chmod 770 /home/production/volume/public
    fi

    if [[ ! -e /home/production/volume/public/images ]]
    then
        mkdir /home/production/volume/public/images
        chown www-data /home/production/volume/public/images
	chmod 770 /home/production/volume/images
    fi

    if [[ ! -e /home/production/volume/tmp ]]
    then
        mkdir /home/production/volume/tmp
        chown www-data /home/production/volume/tmp
	chmod 770 /home/production/volume/tmp
    fi

    if [[ ! -e /home/production/volume/cache ]]
    then
        mkdir /home/production/volume/cache
        chown www-data /home/production/volume/cache
	chmod 770 /home/production/volume/cache
    fi

    if [[ ! -e /home/production/volume/cluster ]]
    then
        mkdir /home/production/volume/cluster
        chown www-data /home/production/volume/cluster
	chmod 770 /home/production/volume/cluster
    fi
    
    if [[ ! -e /home/production/volume/pgdata ]]
    then
        mkdir /home/production/volume/pgdata
        chown postgres /home/production/pgdata
    fi
else
    echo "/home/production/volume does not exist... not creating dirs";
fi


if [ "$MODE" == "DEVELOPMENT" ]; then
        /home/production/cxgn/sgn/bin/sgn_server.pl --fork -r -p 8080
else
    /etc/init.d/sgn start
    touch /var/log/sgn/error.log
  chmod 777 /var/log/sgn/error.log
  tail -f /var/log/sgn/error.log
fi