!/bin/bash

# set API key API_KEY=${GALAXY_DEFAULT_ADMIN_KEY:-fakekey}

# Enable Test Tool Shed echo “.. Setting up conda” 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 Database
echo ".. Starting database"
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
# start Galaxy
echo ".. Starting Galaxy"
# Unset SUDO_* vars otherwise conda run chown based on that
sudo -E -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 120
echo ".. Galaxy is running"

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
    . $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

# install tutorial materials echo “.. Starting installation of the tutorials.” for tutdir in $topicdir/tutorials/* do

echo "-------------------------------------------------------------"
tut=$(basename $tutdir)
echo "Installing tutorial: $tut"
# install tools and workflows
if [ -d $tutdir/workflows/ ];
then
    echo " - Extracting tools from workflows"
    for w in $tutdir/workflows/*.ga
    do
        workflow-to-tools -w $w -o $tutdir/workflows/wftools.yaml -l $tut
        echo " - Installing tools from workflow $(basename $w)" 
        n=0
        until [ $n -ge 3 ]
        do
            shed-tools install -t $tutdir/workflows/wftools.yaml -g "http://localhost:$PORT" -a $API_KEY && break
            n=$[$n+1]
            sleep 5
            echo " - Retrying shed-tools install "
        done        
        rm $tutdir/workflows/wftools.yaml          
    done
    echo " - Installing workflows"
    workflow-install --publish_workflows --workflow_path $tutdir/workflows/ -g "http://localhost:$PORT" -a $API_KEY
else
    echo " - No workflows to install (no directory named workflows present)"
fi

# install reference data? (discussion: do this at build or run time?)
# We are using CVMFS for the moment.
#if [ -f $dir/data-manager.yaml ]
#then
#    echo " - Installing reference data"
#    run-data-managers --config $dir/data-manager.yaml -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD
#else
#    echo " - No reference data to install (no file named data-manager.yaml present)"
#fi

# install tours
if [ -d $tutdir/tours/ ];
then
    echo " - Installing tours"
    for t in $tutdir/tours/*
    do
        fname=$tut-$(basename $t)
        echo "   - Installing tour: $t as $fname"
        cp $t $GALAXY_ROOT/config/plugins/tours/$fname
    done
else
    echo " - No tours to install (no directory named tours present)"
fi

echo " - Finished installation of $tut tutorial"

done

echo “————————————————————-” echo “.. Generating data-library_all.yaml file” cd /tutorials/ python /mergeyaml.py > ./data-library_all.yaml

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

echo ".. Shutting down Galaxy and postgresql"
# stop everything
sudo -E -u galaxy /galaxy-central/run.sh --stop --pidfile /galaxy-central/galaxy_install.pid
rm /galaxy-central/$install_log
service postgresql stop

fi

echo “.. Installation is finished”