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bootstrap.sh
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bootstrap.sh
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#!/bin/bash
echo "**PREPARE BASE SYSTEM**************************************************"
export DEBIAN_FRONTEND=noninteractive
echo "**set timezone*********************************************************"
ln -sf /usr/share/zoneinfo/Europe/Berlin /etc/localtime
dpkg-reconfigure tzdata
echo "**freshen package index************************************************"
apt-get update
apt-get upgrade -y
echo "**install software*****************************************************"
# just a little hack for multiline command with comments
CMD=(
apt-get install -y --no-install-recommends
docker.io
default-jdk
tomcat8
maven
git
)
"${CMD[@]}"
echo "**enable docker support for standard user******************************"
usermod -a -G docker vagrant
echo "**install docker-compose***********************************************"
curl -sSL https://github.com/docker/compose/releases/download/1.23.1/docker-compose-$(uname -s)-$(uname -m) -o /usr/local/bin/docker-compose
chmod +x /usr/local/bin/docker-compose
echo "**INSTALL MASSBANK COMPONENTS******************************************"
echo "**pull up mariadb docker container****************************************"
mkdir /mariadb
cd /vagrant
docker-compose -f compose/mariadb-docker-compose.yml up -d
echo "**fetch data repo******************************************************"
(cd /home/vagrant; \
git clone --depth 1 -q https://github.com/MassBank/MassBank-data.git; \
chown -R vagrant:vagrant MassBank-data)
echo "**compile MassBank webapp**********************************************"
(cd MassBank-Project; mvn install)
cp MassBank-Project/MassBank/target/MassBank.war /var/lib/tomcat8/webapps/
cp MassBank-Project/api/target/api.war /var/lib/tomcat8/webapps/
cp conf/massbank.conf /etc
echo "**update database******************************************************"
MassBank-Project/MassBank-lib/target/MassBank-lib-0.0.1-default/MassBank-lib-0.0.1/bin/RefreshDatabase
echo "**RESTARTING ALL SERVER************************************************"
sed 's|^JAVA_OPTS="-Djava.awt.headless=true.*|JAVA_OPTS="-Djava.awt.headless=true -Xmx4096m -Xms4096m -XX:+UseConcMarkSweepGC"|g' -i /etc/default/tomcat8
systemctl restart tomcat8