Install Atlassian on QNAP

Version 2.0

All rights reserved © 2016, 2017, John McElhaney

Unpublished work © 2016, 2017, John McElhaney


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 Install Atlassian on QNAP 1

Introduction 6

Requirements 6

JIRA 6

Confluence 6

Bitbucket 6

Configuration 1 - All In One 7

Configuration 2 - All In One, Local Database 7

Configuration 3 - Double Duty 8

Configuration 4, Double Duty, Local Database 8

Configuration 5 - Stand Alone 9

Configuration 6 - Standalone, Local Database 9

Install Ubuntu Server 16.04 10

Download Ubuntu Server 10

Create a new VM 10

Start the Ubuntu Installer 11

Configure the Network 12

Setup Users and Passwords 12

Configure the clock 12

Partition Disks 12

Configure the Package Installer (HTTP Proxy) 12

Configure tasksel 13

Software Selection 13

Install GRUB boot loader 13

Complete the Install and reboot 14

First Boot 15

Perform an initial update 15

Update Ubuntu 15

Gather Network Information 15

Install Service Packages 16

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 Install DNS Server 16

Download Atlassian Packages 16

Download the packages (use up-to-date versions) 16

Download the Packages locally 16

Change the packages into executables 17

Install Database Service (MySQL Service) 18

Install Unzip 18

Install MySQL 18

Download the latest MySQL package 18

Install MySQL 18

Secure the MySql Service 19

Setup for External Access (Optional) 19

Restart the MySQL 20

Test the server for the open port 3306 20

Allow root to connect externally 20

Install MySQL Connector 20

Install MySQL Workbench (Optional) 21

Install Databases 21

Install Database Service (PostgreSQL Service) 23

Install PostgreSQL Service 23

Create a new User 23

Create new Databases 23

Additional Notes 24

Install the Atlassian Services 25

Install the JIRA Software package 25

Install the JIRA Package 25

Install the MySQL Java Connector (Required for the MySQL Database) 26

Startup JIRA Instance 26

Install the Confluence Software package 26

Install the Confluence Package 26

Install the MySQL Java Connector (Required for the MySQL Database) 27

Startup Confluence Instance 27

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 Install the Bitbucket Software package 27

Install the Bitbicket Package 27

Install the MySQL Java Connector (Required for the MySQL Database) 28

Startup Bitbucket Instance 28

Configure JIRA 29

Configure the Service 29

Begin the configuration 29

Setup the Database… 30

Install the License 32

Setup the Administrator account 32

Setup Email Notifications 34

Select JIRA Administrator Language 35

Choose an Administrator Avatar 35

Finished and Ready… 36

Configure Confluence 37

Configure the Service 37

Begin the configuration 37

Select additional Add Ons 38

Setup the License 38

Database Configuration 39

Select additional Addons 41

Setup the License 41

Setup the Database 42

Load Content 44

Configure User Management 45

Load Users and Groups from JIRA 47

Finished and Ready… 47

Configure Bitbucket 48

Configure Bitbucket Database 48

Setup License 50

Setup Administrator account 50

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 Finished and Ready… 51

Setup Software Firewall (optional) 52

Finish and Complete 53

Logout and Reboot 53

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Introduction
The QNAP Virtual Machine system is capable of running all three services at once on a
singe Virtual Machine. However, I have found that running three individual Virtual Machines
for each of the services seems to improve response times. Here are a few possible
configurations you might consider.

Keep in mind that the Database service can be located within the Virtual-Machine instance,
located on the QNAP server, or located external to the QNAP Server. Choose the best
Database configuration for your environment.

Determine the configuration that works best for your environment and install the services
accordingly.

Requirements
The Atlassian services are very scalable based on hardware availability. This document will
only focus on what Atlassian considers a small project and small teams.

A small project is considered as;

• 100 individual projects.

• 1000 - 5000 Issues total across all projects.
• 100 - 200 users.

JIRA

The JIRA server will require;

• A recent multicore processor.

• 2GB RAM.
• High Speed Hard Drive (7200 RPM) or SSD. (I personally use Western Digital
Black Series Hard Drives or Samsung 3D NAND SSD Drives).

Confluence

The Confluence server will require;

• Quad Core CPU at greater than 2GHz.

• 6GB RAM.
• 10 GB of Hard Drive storage.

Bitbucket

The Bitbucket server will require;

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 • A recent multicore processor.
• 2GB RAM.

Configuration 1 - All In One

QNAP VM1 Database

This configuration will work but the Virtual Machine must be configured with a large number
of cores and a large RAM pool. This setup tends to have slow initial response times.

With the database server located within the VM instance, external database access is not
required; improving security at a cost of VM resources to power the database.

Configuration 2 - All In One, Local Database

VM1

QNAP

Database

This configuration is the same as above, only relocating the database to the QNAP Server.
While this configuration removes the Database load from the Virtual Machine it reduces the
security of the above configuration because the database must now be externally
accessible (local network). As long as the database is not WAN, (Wide-Area-Network)
accessible this should not be an issue.

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Configuration 3 - Double Duty

VM1 Database

QNAP

VM2 Database

This configuration is somewhat common setup. Again, with the databases located within
the VM instances, no external database access is needed. Because the Bitbucket service
has a relatively low hardware requirement it can piggy-back with the JIRA service. This
leaves the Confluence service its own VM instance.

Configuration 4, Double Duty, Local Database

VM1

QNAP Database

VM2

This configuration is similar to the above with the Database server running natively on the
QNAP. As stated above this exposes the Database server to LAN, (Local-Area-Network)
traffic but also refuses the load on the Virtual Machines.

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Configuration 5 - Stand Alone

VM1 Database

QNAP VM2 Database

VM3 Database

This configuration allows each service to run independently with the Database service local
to the services. This has a larger memory footprint and may exceed the QNAP’s onboard
memory. During testing the system was consuming 92% of the system’s RAM at any given
time.

Configuration 6 - Standalone, Local Database

VM1

VM2

QNAP

VM3

Database

This configuration allows each service to run independently with the Database service local
to the services. This has a larger memory footprint and may exceed the QNAP’s onboard
memory. During testing the system was consuming 92% of the system’s RAM at any given
time.

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Install Ubuntu Server 16.04

Download Ubuntu Server

Open a web browser and navigate to the Ubuntu Server download page, and download the
ubuntu-16.04.3-server-amd64.iso (or latest) ISO file.

https://www.ubuntu.com/download/server

Once downloaded, upload the file into an accessible file location on the QNAP

Create a new VM
From the QNAP Admin Screen, navigate to the Virtualization Station (3.0), and click ‘Click
VM’.

Fill out the new VM form;

• VN Name: the name of the new Virtual-Machine

• Description: optional
• OS Type: Linux
• Version: Ubuntu 16.04 (or later)

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 • CPU Cores: 2 (optional)
• Memory: 2GB (optional)
• CD Image: locate the Ubuntu ISO previously uploaded to the QNAP
• HDD Location: Navigate to a good place to store the VM Hard Drive file

Click OK to begin. Finally click the ‘Power’ Button to start the Virtual-Machine.

Double click the Screen preview to open the Virtual Machine in a VNC window. We will be
doing most of the install from the VM VNC.

Start the Ubuntu Installer

• Select the desired Language.

• Next Start the Install.
• Select the install process language.
• Select the Country.
• Configure the Keyboard.

Allow components to install…

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Configure the Network

• Enter the host name for the server.

Setup Users and Passwords

• Enter a superuser name.

• Enter a account name (same as Superuser).
• Enter a Password.
• Re-enter a password.
• Encrypt Home Directory: no.

Allow setup to complete.

Configure the clock

• Confirm the timezone.

Partition Disks

• Select Guided Partitioning.

• Select Guided - use entire disk and set up LVM.
• Select the disk to partition.
• Confirm Write Changes to the disk.
• Confirm the amount of the Disk Partition.
• Finish Partitioning and write changes to the disk.
• Write changes to the disk.

Allow the configuration to complete.

Configure the Package Installer (HTTP Proxy)

• Leave blank for none.

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 Allow the configuration to complete.

Configure tasksel

• Select Install Security Updates Automatically.

Allow the configuration to complete.

Software Selection

• Select Standard System Utilities.

• No other packages at this time.

Allow the configuration to complete.

Install GRUB boot loader

Select to install the GRUB boot loader to the Master Boot Record; YES.

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Complete the Install and reboot
From the Virtual Machine controller, eject the Ubuntu Installer ISO image.

In the Virtual-Machine select continue to Reboot to the first boot.

Allow the installer to complete.


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First Boot

Perform an initial update

Login using the Super User name and password.

Update Ubuntu

sudo apt-get update

Wait…

sudo apt-get upgrade

And Wait… When prompted select ‘y’ to install the upgrades.

Wait…

When finished, reboot (optional).

sudo reboot

And Wait…

Gather Network Information

Get the new Virtual Machines MAC address

ifconfig

If necessary reserve a static IP address to the Virtual Machine’s MAC Address. This will
allow Port Forwarding to a static IP address. Once the MAC Address is reserved, reboot.

sudo reboot

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Install Service Packages

Install DNS Server

Install DNS Server for dynamic host name

sudo apt-get avahi-daemon

Follow prompts.

sudo reboot

Check for external DNS access to ‘atlassian.local’. The correct IP should be returned.

Download Atlassian Packages

Download the packages (use up-to-date versions)

Navigate to the Atlassian product pages and verify the download links.

Download the Packages locally

wget https://www.atlassian.com/software/jira/downloads/
binary/atlassian-jira-software-7.4.2-x64.bin

wget https://www.atlassian.com/software/confluence/
downloads/binary/atlassian-confluence-6.3.2-x64.bin

wget https://www.atlassian.com/software/stash/downloads/
binary/atlassian-bitbucket-5.2.2-x64.bin

(Optional packages)

wget https://www.atlassian.com/software/jira/downloads/
binary/atlassian-servicedesk-3.6.2-x64.bin

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Change the packages into executables

sudo chmod +x atlassian-jira-software-7.4.2-x64.bin

sudo chmod +x atlassian-confluence-6.3.2-x64.bin

sudo chmod +x atlassian-bitbucket-5.2.2-x64.bin

sudo chmod +x atlassian*.*

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Install Database Service (MySQL Service)
Atlassian uses several types of Database services. While PostgreSQL is the default service,
MySQL can be used as well. This chapter covers the MySQL setup.

Install Unzip
If the Services will be using the MySQL Database, continue. If using the default
PostgreSQL, skip.

sudo apt-get install unzip

Follow prompts.
Install either PostgreSQL Service or MySQL Service. PostgreSQL is the default service for
Atlassian products.

Install MySQL
If the Services will be using the MySQL Database, continue. If using the default
PostgreSQL, skip.

Download the latest MySQL package

curl -OL https://dev.mysql.com/get/mysql-apt-

config_0.8.3-1_all.deb

Install MySQL

sudo dpkg -i mysql-apt-config*

sudo apt-get update

rm mysql-apt-config*

sudo apt-get install mysql-server

Follow prompts.

Enter root (MySql): password

Again: password
Check that the Mysql service is installed and running.

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 systemctl status mysql

Verify MySQL login Credentials:

mysql -p -u root

And then leave MySQL prompt

quit;

Secure the MySql Service

mysql_secure_installation

Follow prompts.

Setup for External Access (Optional)

Tell MySQL to listen for external connections (less secure)

sudo nano /etc/mysql/mysql.conf.d/mysqld.cnf

Change bind-address from 127.0.0.1 to 0.0.0.0

bind-address = 127.0.0.1

To

bind-address = 0.0.0.0

Add the following lines:

validate_password_policy=LOW

max_allowed_packet = 512M

innodb_log_file_size = 2G

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 • Control-x to exit
• Yes, save changes
• Save under same name

Restart the MySQL

Restart the MySQL service to have changes take effect

sudo systemctl restart mysql

systemctl status mysql

The System should indicate that the MySQL Service is active. If not double check your
mysql.cnf file for edit errors.

Test the server for the open port 3306

Using a external tool, (i.e.: Network Utility), port scan the server for the post 3306. This will
prove that the MySQL server is listening for external connections.

Open TCP Port: 3306 mysql

Allow root to connect externally

mysql –u root -p

GRANT ALL PRIVILEGES ON *.* TO root@'%' IDENTIFIED BY

'password';

GRANT GRANT OPTION ON *.* TO ‘root’@‘%’;

FLUSH PRIVILEGES;

quit;

Install MySQL Connector

If we are using the MySQL Database, we will need the MySQL Java Connector for JIRA and
Confluence to work correctly.

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 wget https://dev.mysql.com/get/archives/mysql-connector-
java-5.1/mysql-connector-java-5.1.36.zip

unzip mysql-connector-java-5.1.36.zip

unzip mysql-connector-java-*.zip

rm mysql-connector-java-5.1.36.zip

rm mysql-connector-java-*.zip

This will be further installed in later steps.

Install MySQL Workbench (Optional)

Install MySQL Workbench to service MySQL Database externally.

https://www.mysql.com/products/workbench/

Install Databases
Databases can be installed via the external MySQL Workbench or via the command line.

If you are installing via Command Line only, use the following MySQL Commands to install
the required databases. Pay close attention to the position of the line terminator ‘;’.

mysql -p -u root

CREATE DATABASE Atlassian_JIRA

DEFAULT CHARACTER SET utf8

DEFAULT COLLATE utf8_bin;

GRANT ALL PRIVILEGES ON Atlassian_JIRA.* TO

'Atlassian_JIRA'@'localhost' IDENTIFIED BY ‘password';

CREATE DATABASE Atlassian_Confluence

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 DEFAULT CHARACTER SET utf8

DEFAULT COLLATE utf8_bin;

GRANT ALL PRIVILEGES ON Atlassian_Confluence.* TO

'Atlassian_Confluence'@'localhost' IDENTIFIED BY
‘password';

CREATE DATABASE Atlassian_Bitbucket

DEFAULT CHARACTER SET utf8

DEFAULT COLLATE utf8_bin;

GRANT ALL PRIVILEGES ON Atlassian_Bitbucket.* TO

'Atlassian_Bitbucket'@'localhost' IDENTIFIED BY 'password';

quit;

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Install Database Service (PostgreSQL Service)
Atlassian uses several types of Database services. While PostgreSQL is the default service,
MySQL can be used as well. This chapter covers the MySQL setup.

Install PostgreSQL Service

sudo apt-get install postgresql postgresql-contrib

Create a new User

Create a new PostgreSQL User, (use double dashes. Use lowercase names);

sudo —u postgres createuser atlassian —interactive —

pwprompt

• Password and confirmation

• Super User?: yes
• Allowed to create databases: yes
• Allowed to create new roles: no

Create new Databases

Create a Database for each service, (use lowercase names)

sudo -u postgres createdb -O atlassian atlassian_jira

sudo -u postgres createdb -O atlassian atlassian_confluence

sudo -u postgres createdb -O atlassian atlassian_bitbicket

sudo -u postgres createdb atlassian_jira

sudo -u postgres createdb atlassian_confluence

sudo -u postgres createdb atlassian_bitbicket

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 This can be verified by;

sudo -I -u postgres

psql

\du

\list

\q

This will list all of the databases and users. The result should match this image.

Additional Notes
Note; this command can be used to delete a user or database;

sudo -u postgres dropuser Atlassian_JIRA

sudo -u postgres dropdb Atlassian_JIRA

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Install the Atlassian Services
Install each package but do not start the service. We will need to make additional
adjustments before the service will function.

Install the JIRA Software package

Install the JIRA Package

sudo ./atlassian-jira-software-7.4.1-x64.bin

sudo ./atlassian-jira-software-*.bin

• Select option ‘o’ to install onto this computer.

• Select option ‘2’ to Custom Install.
• Select default directory.
• Select default directory.
• Do not use the default Port 8080. Select new HTTP Port 7995. Because the
QNAP interface uses port 8080 for the administration panel we want to change
the JIRA HTTP port to something different.
• Do use the default control port: 8005
• Select Yes to use JIRA as a Service.
• Select option ‘i’ to begin install.

Note that the service runs on the following ports:

• HTTP Port: 7995 (default 8080)

• RMI Port: 8005

If using the MySQL database; when Finished the installer will ask if you want to start the
service now; select ‘no’. We will need to install the MySQL Java Connector to use the
MySQL database.

• Start JIRA Software now: no

Otherwise if using the PostgreSQL select yes to start the JIRA service now. JIRA is now
ready for Service.

• Start JIRA Software now: yes

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 If the database service is PostgreSQL, proceed to the next setup; JIRA is ready for
configuration.

Install the MySQL Java Connector (Required for the MySQL Database)

If we are using the MySQL Database, we will need the MySQL Java Connector for JIRA and
Confluence to work correctly.

sudo cp mysql-connector-java-5.1.36/mysql-connector-
java-5.1.36-bin.jar /opt/atlassian/jira/lib/

Startup JIRA Instance

JIRA is now ready for the first startup and configuration.

sudo /opt/atlassian/jira/bin/startup.sh

This can be verified by using the command;

systemctl status JIRA

Install the Confluence Software package

Install the Confluence Package

sudo ./atlassian-confluence-6.3.2-x64.bin

sudo ./atlassian-confluence-*.bin

• Select option ‘o’ to install onto this computer.

• Select option ‘1’ to Express Install.
• Select option ‘i’ to begin install.

Note that the service runs on the following ports:

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 • HTTP Port: 8090
• RMI Port: 8000

When Finished the installer will ask if you want to start the service now; select ‘no’. We will
need to install the MySQL Java Connector to use the MySQL database.

• Start Confluence Software now: no

Install the MySQL Java Connector (Required for the MySQL Database)

If we are using the MySQL Database, we will need the MySQL Java Connector for JIRA and
Confluence to work correctly.

sudo cp mysql-connector-java-5.1.36/mysql-connector-
java-5.1.36-bin.jar /opt/atlassian/confluence/confluence/
WEB-INF/lib

sudo cp mysql-connector-java-*/mysql-connector-java-*.jar /
opt/atlassian/confluence/confluence/WEB-INF/lib

Startup Confluence Instance

Confluence is now ready for the first startup and configuration.

sudo /opt/atlassian/confluence/bin/startup.sh

Install the Bitbucket Software package

Install the Bitbicket Package

sudo ./atlassian-bitbucket-5.2.2-x64.bin

sudo ./atlassian-bitbucket-*.bin

• Select option ‘1’ to install onto this computer.

• Select option ‘1’ to install a Server instance.

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 • Select default install location: /opt/atlassian/bitbucket/5.2.2
• Select run as service: yes
• Select ‘i’ to start the install process.

Note that the service runs on the following ports:

• HTTP Port: 7990

• Search Ports: 7992 & 7993

When Finished the installer will ask if you want to start the service now; select ‘no’. We will
need to install the MySQL database use the service.

• Start Bitbucket Software now: no

Install the MySQL Java Connector (Required for the MySQL Database)

If we are using the MySQL Database, we will need the MySQL Java Connector for JIRA and
Confluence to work correctly.

sudo cp mysql-connector-java-5.1.36/mysql-connector-
java-5.1.36-bin.jar /opt/atlassian/bitbucket/5.2.2/lib/

sudo cp mysql-connector-java-*/mysql-connector-java-*.jar /
opt/atlassian/bitbucket/5.2.2/app/WEB-INF/lib

Startup Bitbucket Instance

Bitbucket is now ready for the first startup and configuration.

sudo /opt/atlassian/bitbucket/5.2.2/bin/start-bitbucket.sh


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Configure JIRA

Configure the Service

Navigate your web browser to the web service. If the Service will only be used on a LAN,
(Local-Area-Network), use the address; (the default is 8080).

http://atlassian.local:7995

If the Service will be accessed via WAN, (Wide-Area-Network), or via the Internet, use the
registered DNS address; (the default is 8080).

http://atlassian.myserver.com:7995

Begin the configuration

• Select “I’ll set it up myself”…

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Setup the Database…

For MySQL Setup -

• Select the Database Type: MySQL

• Enter the Database Server Host Name: localhost
• Use the default Database Port: 3306
• Select the Database: Atlassian_JIRA
• Set the Database’s Authorized username, (do not use root): Atlassian_JIRA
• Set the Database’s Authorized user password: password

For PostgreSQL Setup -

• Select the Database Type: PostgreSQL

• Enter the Database Server Host Name: localhost
• Use the default Database Port: 5432

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 • Select the Database: atlassian_jira
• Set the Database’s Authorized username: atlassian
• Set the Database’s Authorized user password: password
• Schema: public

Test the connection… Correct any issues that are reported.

Click Next.

The Database install will take several minutes. Do not interrupt the process. If the process
hangs try reloading the page using the http address, not reload.Set the Service Title.

• Set the Mode: Private.

• Set the Base URL: This is the fully qualified DNS address of the server via
WAN or LAN. This MUST be set correctly before continuing. For external
service access use the WAN address. For Internal or Local use only use the
LAN address.

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Install the License

Click Next and wait while the License Installs.

Setup the Administrator account

• Full Name: as needed

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 • Email Address: as needed
• User Name: as needed
• Password: password
• Confirm Password: password

Click Next to continue.

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Setup Email Notifications

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Select JIRA Administrator Language

Choose an Administrator Avatar

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Finished and Ready…
JIRA is now ready for service.


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Configure Confluence

Configure the Service

Navigate your web browser to the web service. If the Service will only be used on a LAN,
(Local-Area-Network), use the address;

http://atlassian.local:8090

If the Service will be accessed via WAN, (Wide-Area-Network), or via the Internet, use the
registered DNS address;

http://atlassian.myserver.com:8090

Begin the configuration

• Select Product Installation.

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Select additional Add Ons

• Select additional admins if needed. Click Next to continue.

Setup the License

• Enter the License Key.

• Click Next and wait. It will take some time for the license to install.

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Database Configuration

• Select MySQL.
• Click on the External Database button.

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• Select the Direct JDBC to use the MySQL Java Connector.

• Driver Class Name: com.mysql.jdbc.Driver

• Database URL: jdbc:mysql://localhost/Atlassian_Confluence
• Username: Atlassian_Confluence
• Password: password

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 Click the Next button. And correct any issues.

The Database install will take several minutes. Do not interrupt the process. If the process
hangs try reloading the page using the http address, not reload.Set the Service Title.

Select additional Addons

• Select additional admins if needed. Click Next to continue.

Setup the License

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 • Enter the License Key.
• Click Next and wait. It will take some time for the license to install.

Setup the Database

• Select the MySQL Database

• Click the “External Database button.

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• Select the JDBC Connection. Click on the Direct JDBC button.

Configure the JDBC (Java Database Connector).

• Driver class name:

• Database URL:
• User Name:
• Password:

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Load Content

Select the Initial content desired; The example site will have several templates, otherwise
the Empty Site will provide a blank slate.

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Configure User Management

Users can be managed via Confluence but it is recommended to use the JIRA service
instance to manage all Users and Permissions. Select Connect to JIRA

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Load Users and Groups from JIRA

After the Sync completes, press next.

Press Start.

Finished and Ready…

Confluence is now ready for service.

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Configure Bitbucket

Configure Bitbucket Database

• Select the External Database.

• Click Next.

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 • Language: As needed.
• Database: External
• Database Type: MySQL
• Hostname: localhost
• Port: 3306 (default)
• Database name: Atlassian_Bitbucket
• Database Username: Atlassian_Bitbucket
• Database Password: password

Test the connection… Correct any issues that are reported.

Click Next.

The Database install will take several minutes. Do not interrupt the process. If the process
hangs try reloading the page using the http address, not reload.Set the Service Title.

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Setup License

Click Next and wait while the License Installs.

Setup Administrator account

• Username: (as needed)

• Full Name: (as needed)
• Email Address: (as needed)
• Password: password
• Confirm Password: password
Integrate with JIRA or Go to Bitbucket.

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Finished and Ready…
Bitbucket is now ready for service.

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Setup Software Firewall (optional)
Execute the following commands to enable the software firewall.

Turn on the software firewall

#sudo ufw enable

Enable external access to the MySQL Database (optional).

#sudo ufw allow 3306

Enable external access to the Postgres Database (optional).

#sudo ufw allow 5432

Allow access to the JIRA service

#sudo ufw allow 7995

Allow access to the Confluence service.

#sudo ufw allow 8090

Allow access to the BitBucket service.

#sudo ufw allow 7990

Add any additional ports that may be required…

© 2016, 2017 John McElhaney Page 52 of 53

Finish and Complete

Logout and Reboot

sudo reboot

• Wait several minutes to stop all services.

• Wait several minutes for the hardware to reset.
• Wait several minutes for the services to start.

© 2016, 2017 John McElhaney Page 53 of 53