install_tools_wrapper.sh

#!/bin/bash

# Enable Test Tool Shed
echo "Enable installation from the Test Tool Shed."
export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml

. /tool_deps/_conda/etc/profile.d/conda.sh
conda activate base

if pgrep "supervisord" > /dev/null
then
    echo "System is up and running. Starting with the installation."
    export PORT=80
else
    # start Galaxy
    export PORT=8080
    service postgresql start
    install_log='galaxy_install.log'

    # wait for database to finish starting up
    STATUS=$(psql 2>&1)
    while [[ ${STATUS} =~ "starting up" ]]
    do
      echo "waiting for database: $STATUS"
      STATUS=$(psql 2>&1)
      sleep 1
    done

    echo "starting Galaxy"
    # Unset SUDO_* vars otherwise conda run chown based on that
    sudo -E -H -u galaxy -- bash -c "unset SUDO_UID; \
        unset SUDO_GID; \
        unset SUDO_COMMAND; \
        unset SUDO_USER; \
        ./run.sh -d $install_log --pidfile galaxy_install.pid --http-timeout 3000"

    galaxy_install_pid=`cat galaxy_install.pid`
    galaxy-wait -g http://localhost:$PORT -v --timeout 600
fi

# Create the admin user if not already done
# Starting with 20.05 this user is only created at first startup of galaxy
# We need to create it here for Galaxy Flavors = installing from Dockerfile
if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]]
    then
        (
        cd $GALAXY_ROOT_DIR
        . $GALAXY_VIRTUAL_ENV/bin/activate
        echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing"
        python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \
        -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY"
        )
fi

shed-tools install -g "http://localhost:$PORT" -a fakekey -t "$1"

exit_code=$?

if [ $exit_code != 0 ] ; then
    if [ "$2" == "-v" ] ; then
        echo "Installation failed, Galaxy server log:"
        cat $install_log
    fi
    exit $exit_code
fi

if ! pgrep "supervisord" > /dev/null
then
    # stop everything
    sudo -E -H -u galaxy ./run.sh --stop --pidfile galaxy_install.pid
    rm $install_log
    service postgresql stop
fi