This is the script I run when setting up a new Minecraft server.

minecraft.sh

#!/bin/bash

# The name of the .jar file for the latest version.
MINECRAFT_LATEST="minecraft_server.1.7.9.jar"
# The URL for the lates version of the minecraft server
MINECRAFT_LATEST_LINK="https://s3.amazonaws.com/Minecraft.Download/versions/1.7.9/minecraft_server.1.7.9.jar"
# The screen name for the Minecraft Server
MINECRAFT_SCREEN_NAME="Minecraft"

# Setup some variables
pwd=$(pwd)
mc="$pwd/minecraft"

echo "Setting up Minecraft"

# Create the Minecraft folder if it doesn't exist
if [ ! -d $mc ]; then
  echo "Creating $mc"
  mkdir $mc
fi
cd $mc

# Create the .versions folder if it doesn't exist
versions="$mc/.versions"
if [ ! -d "$versions" ]; then
  echo "Creating $versions"
  mkdir "$versions"
fi

# Download the lates Minecraft
if [ ! -f "$versions/$MINECRAFT_LATEST" ]; then
  echo "Downloading Minecraft $MINECRAFT_LATEST"
  cd $versions
  wget $MINECRAFT_LATEST_LINK -O $MINECRAFT_LATEST
  cd $mc
else
  echo "$MINECRAFT_LATEST already exists"
fi

cd $mc

# Remove current link and link latest to server.jar
if [ -f "$mc/server.jar" ]; then
  rm "$mc/server.jar"
fi
ln -s "$versions/$MINECRAFT_LATEST" "$mc/server.jar"

# Create start.sh script
if [ ! -f "$mc/start.sh" ]; then
  echo "screen -d -m -S $MINECRAFT_SCREEN_NAME java -jar server.jar -Xmx4G -Xms4G nogui" > "$mc/start.sh"
  chmod +x "$mc/start.sh"
fi
# Create stop.sh script
if [ ! -f "$mc/stop.sh" ]; then
  echo "screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"stop \$(printf '\r')\"" > "$mc/stop.sh"
  chmod +x "$mc/stop.sh"
fi

# Create backup.sh script
if [ ! -f "$mc/backup.sh" ]; then
  echo "
    screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"say Performing backup \$(printf '\r')\"
    screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"save-off \$(printf '\r')\"
    screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"save-all \$(printf '\r')\"
    sleep 3

    # Backup
    backups=\"$mc/../backups\"

    if [ ! -d \$backups ]; then
      mkdir \$backups
    fi

    cd $mc

    # Delete file older than 5 days
    find \$backups/*.tar.gz -mtime +5 -exec rm {} \;

    NOW=$(date +"%Y-%m-%d")
    tar -cpvzf \$backups/minecraft-\$NOW.tar.gz $mc --exclude='logs/*' --exclude='*.log' --exclude='.versions'

    # Done
    sleep 3
    screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"save-on \$(printf '\r')\"
    screen -r $MINECRAFT_SCREEN_NAME -p 0 -X stuff \"say Backup complete. \$(printf '\r')\"
  " > "$mc/backup.sh"
  chmod +x "$mc/backup.sh"
fi

echo "Done"