Installation Manual
The following sections can be used for advanced installation options that are not covered by the Pladipus installer.
Prerequisites
For Pladipus to run correctly, the following is needed :
- Java 8 must be installed
- Connection to a MySQL database with create privileges (not included in installer)
- Connection to an ActiveMQ host on an available post (optional in installer + automatic download)
- Either Pladipus Management or Executor modes
Installing Pladipus
Download the pladipus installer here and follow the on screen messages.
In the case of a headless installation, please download either the zipped installation folder here and extract the folder contents in the user home directory.
Note: The demonstration video shows how to install Pladipus using the installer.
Settings
The configuration can be done using the installer.
They can also be changed manually, for example when a headless install is required.
The configuration file can be found and edited at $USER_HOME/pladipus/config/network.properties
Database Settings
| Property | Definition | Default value |
|---|---|---|
| db.host | The hostname or IP-adress of the mySQL server | localhost |
| db.port | The port that the mySQL-service is listening on | 3306 |
| db.login | The account that can connect with both read and create rights to the mySQL database | root |
| db.pass | The password for the mySQL login (if any) |
ActiveMQ Settings
| Property | Definition | Default value |
|---|---|---|
| AMQ.host | The hostname or IP-adress of the activeMQ server | localhost |
| AMQ.port.queue | The port that the activeMQ-service is listening on to withdraw jobs from the queue | 3389 |
| AMQ.port.jmx | The port that is used to access the management console (don’t change unless the default port is in use) | 1099 |
| AMQ.version | The currently used activeMQ version | 5.11.1 |
| AMQ.max.retry | The amount of times a job can be relaunched due to failure before being discarded by the system | 5 |
Other Settings
| Property | Definition | Default value |
|---|---|---|
| logging.level | The level output that will be displayed on the console | INFO |
| app.classpath | The folder where pladipus steps will be loaded from | $USER_HOME/.compomics/pladipus/external/ |
Installing MySQL
This tutorial will demonstrate how to install MySQL on a Windows machine, but similar versions are also available for Linux.
Using an installer
The MySQL database does offer an excellent installer. The wizard will guide you and create the my.ini configuration file and installs MySQL as a service. This option is the recommended solution for novice users.
- Navigate to the downloads page.
- Find the MySQL Community Edition
- Select the MySQL Community Server and continue to download the specific MySQL Installer for your system
Note : You do not have to create a login on the MySQL website ! There is a small link at the bottom of the page saying ‘No thanks, just start my download.’
- Double click the .msi installer. If a previous version of MySQL was detected, it will automatically update
- During the installation, install or upgrade the MySQL server.
Manual Installation
More advanced users may prefer a manual installation, as the user has more control over how and when MySQL runs.
- Navigate to the MySQL Community Server for your operating system from the downloads page
- Download the ‘Without installer’ version.
- Extract the ZIP file to a destination of your choice and rename the unzipped folder to ‘mysql’.
Note : MySQL can be installed anywhere on your system. If you want a lightweight installation, you can remove every sub-folder except for bin, data, scripts and share.
Configuration
- Locate or create the my.ini file in the mysql folder.
- Add or update the following statements:
# The TCP/IP Port the MySQL Server will listen on
port=[insert the port, this is by default 3306]
# IP address to bind to.
bind-address=[0.0.0.0 OR the IP address of the MySQL server]
Note : Updating the bind-address is mandatory. It otherwise defaults to localhost, disallowing all access from outside the server.
Starting the server
- Open a command line window and navigate to the bin folder inside the MySQL folder
- Launch the following command:
C:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld
Stopping the server
- Open a command line window and navigate to the bin folder inside the MySQL folder
- Launch the following command:
C:\Program Files\MySQL\MySQL Server 5.0\bin\mysqladmin" -u root shutdown
Installing ActiveMQ
It is highly recommended to use the Pladipus installer or the zipped archive to install ActiveMQ. The configuration will automatically be updated doing so. On a fresh, manual install, all changes made to this configuration have to be reflected in the Pladipus Settings as well. For more advanced configuration parameters, please consult the ActiveMQ website.
Manually changing default activeMQ settings
- Locate the configuration file in the ‘conf’ folder of ActiveMQ. This can be found at
$USER_HOME/pladipus/activeMQ/apache-activemq-5.11.1/conf/activemq.xmlwhen using one of the Pladipus installation options
Changing the ActiveMQ port for queues
- Locate the following XML-entry in the config file:
<transportConnectors>
<transportConnector name="openwire" uri="tcp://localhost:3389?jms.prefetchPolicy.queuePrefetch=1"/>
</transportConnectors>
- replace 3389 with the new, available and open port of your choice
Changing the ActiveMQ port for the jmx management console
- Locate the following XML-entry in the config file:
<managementContext>
<managementContext connectorPort="1099" createConnector="true"/>
</managementContext>
- Replace 1099 with the new, available and open port of your choice