|Original author(s)||K Verheggen, D Maddelein, N Hulstaert, L Martens, H Barsnes, M Vaudel|
|Citation||Verheggen et al., J Proteome Res. 2016, 15(3):707-12|
|Input format||depending on process|
|Output format||depending on process|
|Operating system||Windows, Linux|
|License||Apache License, Version 2.0|
The CompOmics Pladipus system is an affordable cluster computing framework allowing for distributed processing, management and analyses for bio-informatics pipelines. It was developed at the CompOmics group led by Prof.Dr. Martens. The CompOmics group is part of both Ghent University and VIB. Pladipus is being continuously used in house for the reprocessing of public proteomics data and the distribution of emberassingly parallel tasks through a compute GRID. It allows for idle hardware to be plugged into the system and aid to disperse the otherwise heavy computational workload.
Pladipus can straightforwardly be installed and operated thanks to its user friendly graphical interface, allowing complex bioinformatics tasks to be easily run on a network instead of a single computer. As a result, any scientist can benefit from the increased computational efficiency provided by distributed computing, hence empowering them to tackle more complex bioinformatics challenges. Notably, it enables the large scale reprocessing of publicly available data, supporting the scientific community in mining these for novel discoveries.
Supported Operating Systems
Pladipus can be installed on both Windows and Linux machines. As all source code is written in java, MacOSx is theoretically also supported, but this has not been tested or applied as of yet.
Download the latest 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](Pladipus-Demo) shows how to install Pladipus using the installer.
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 `$USER_HOME/pladipus/config/network.properties`
|db.host||The hostname or IP-adress of the mySQL server||localhost|
|db.port||The port that the mySQL-service is listening on||3306|
|db.login||The account that can connect with both read and create rights to the mySQL database||root|
|db.pass||The password for the mySQL login (if any)|
|AMQ.host||The hostname or IP-adress of the activeMQ server||localhost|
|AMQ.port.queue||The port that the activeMQ-service is listening on to withdraw jobs from the queue||3389|
|AMQ.port.jmx||The port that is used to access the management console (don't change unless the default port is in use)||1099|
|AMQ.version||The currently used activeMQ version||5.11.1|
|AMQ.max.retry||The amount of times a job can be relaunched due to failure before being discarded by the system||5|
|logging.level||The level output that will be displayed on the console||INFO|
|app.classpath||The folder where pladipus steps will be loaded from||$USER_HOME/.compomics/pladipus/external/|
To operate and use pladipus, please refer to the Pladipus wiki.
- Verheggen et al. J Proteome Res.2016, 15(3):707-12 pubmed