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Setting up the Bee Workflow Manager

Installation Prerequisites

  • Linux or MacOS Operating System
  • Java 7 runtime


The workflow manager is distributed in a .tar bundle. This bundle should be extracted in the target directory.

NOTE: Currently this .tar bundle is not yet available for download. In the meantime, the compiling screeningbee workflow manager guide should be followed to obtain the bundle. After building the project the bundle is available in the bee-workflowmanager/build/distributions/ directory.


The etc directory of the installation contains all the configuration files which should be set. These are:

  • bee.config: contains configuration options of the java virtual machine which runs the workflow manager
  • log4j.xml, logback.xml: contains logging settings
  • system.config: contains the basic settings of the workflow manager
  • internals.config: contains settings which are useful for the fine tuning of the system
  • openbis.config, filesystem.config contains the storage dependent settings
  • localexecution.config, drmaa.config, lsf.config: contains the settings of the chosen computing resources

In the first step of the configuration the *_skeleton files should be renamed removing the _skeleton suffix. The configuration files contain the descriptions of the configuration values as comments, and where possible a reasonable default value. For many settings bee will use a default value if the parameter is omitted. This is typically mentioned in the configuration comments.

In the system.config file, the configuration file of the storage and computing resource should be selected according the desired system setup. The other storage and computing resource configuration files are ignored (therefore they should not be set).


After configuring the workflow manager, it should be ready for startup. For managing start, stop, etc, the script should be used. The script accepts the following parameters: start, stop, restart, status, mstatus. I.e. ./ start will start the daemon, and ./ stop will stop the daemon.

Monitoring the workflow manager

The log folder of the installation contains the log files generated by the workflow manager. The main log file is the bee_log.txt file, which shows the ongoing details related to processing, depending on the logging configuration (if it is set to “debug”). The other log file, startup_log.txt contains only the log messages which were not caught by the logging system, i.e. JVM runtime exceptions.

beewm/user/setting_up_the_workflow_manager.txt · Last modified: 2016/05/17 16:17 (external edit)