a

highspec/startup.sh

+#!/bin/bash
+
+CURRDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# update yum
+yum update -y
+
+# install dependencies
+wget $PBZIP_BASE_URL/$PBZIP_PACKAGE
+yum install $BASIC_DEPENDENCIES $PBZIP_PACKAGE -y
+rm $PBZIP_PACKAGE
+
+# get Neo4J
+wget $NEO4J_DOWNLOAD_URL
+tar -xvf artifact.php?name=$NEO4J_SETUP_FILE
+rm artifact.php?name=$NEO4J_SETUP_FILE -f
+mv $NEO4J_VERSION /var/lib/
+
+export NEO4J_HOME=/var/lib/$NEO4J_VERSION
+
+# get apoc plugin
+wget $APOC_URL
+mv $APOC_VERSION $NEO4J_HOME/plugins/
+
+### make few config changes for Neo4J
+for line in `cat $CURRDIR/neo4j.conf`; do
+    sed -i -e "1i$line\\" $NEO4J_HOME/conf/neo4j.conf
+done
+
+# provide ownership to ec2-user user
+chown -R ec2-user:ec2-user $NEO4J_HOME
+
+# get the SSD device name
+device=$(lsblk | grep nvme0n1 | cut -d' ' -f1)
+
+# create an ext4 partition on the disk
+mkfs.ext4 -E nodiscard -m0 /dev/$device
+
+# create a mount point
+mountpoint=/media/disk1
+sudo mkdir -p $mountpoint
+
+# mount the device
+mount -o discard /dev/$device $mountpoint
+
+# provide ownership to ec2-user user
+chown -R ec2-user:ec2-user $mountpoint
+
+# get compressed graph db from S3
+echo "Getting compressed graph db from S3 - START" 
+date
+aws s3 cp s3://ebi-pdbe/neo4j/graph.db.tgz $mountpoint/
+date
+echo "Getting compressed graph db from S3 - END" 
+
+# create directories for neo4j data
+mkdir -p $mountpoint/neo4j_data/databases/graph.db
+mkdir -p $mountpoint/neo4j_data/dbms
+graphdb_path=$mountpoint/neo4j_data/databases/graph.db
+mv $mountpoint/graph.db.tgz $mountpoint/neo4j_data/databases/graph.db/
+
+# uncompress graph data
+echo "Uncompress graph db - START"
+cd $mountpoint/neo4j_data/databases/graph.db
+date
+pbzip2 -dc graph.db.tgz | tar x
+date
+rm graph.db.tgz
+echo "Uncompress graph db - END"
+
+# Change Neo4J config to pick data from new location
+sed -i -e '1idbms.directories.data='${mountpoint}'/neo4j_data\' $NEO4J_HOME/conf/neo4j.conf
+
+echo "Starting Neo4J"
+sudo -u ec2-user $NEO4J_HOME/bin/neo4j start
+

highspec/userdata_script

+#!/bin/bash
+
+yum update -y
+yum install git -y
+
+git clone https://gitlab.ebi.ac.uk/sreenath/pdbe-neo4j-aws.git
+cd pdbe-neo4j-aws
+chmod -R 755 .
+./setup.sh highspec

playground/userdata_script

+#!/bin/bash
+
+yum update -y
+yum install git -y
+
+git clone https://gitlab.ebi.ac.uk/sreenath/pdbe-neo4j-aws.git
+cd pdbe-neo4j-aws
+chmod -R 755 .
+./setup.sh playground