This tool keeps track of the status of a biopet pipeline.

It also possible to push the status. For this a PIM host should be provided.


PipelineStatus requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of PipelineStatus here. To generate the usage run:

java -jar <PipelineStatus_jar> --help


Default this tool will create the output just once. To do this continuously the -f argument should be given.

This tool has also support for PIM, see examples for this.


This will generate a default status check and trying to auto detect the graph:

java -jar <PipelineStatus_jar> \
-d <pipeline_dir> \
-o <output_dir>

This will follow the pipeline and update the results each interval:

java -jar <PipelineStatus_jar> \
-d <pipeline_dir> \
-o <output_dir> \

To push to PIM this should be added:

java -jar <PipelineStatus_jar> \
-d <pipeline_dir> \
-o <output_dir> \
-f \
--pimHost <pim_url>


Usage for PipelineStatus:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
--pipelineDir, -d yes no Output directory of the pipeline
--outputDir, -o yes no Output directory of this tool
--depsFile no no Location of deps file, not required
--follow, -f no no This will follow a run
--refresh no no Time to check again, default set on 30 seconds
--completePlots no no Add complete plots, this is disabled because of performance. Complete plots does show each job separated, while compressed plots collapse all jobs of the same type together.
--skipCompressPlots no no Disable compressed plots. By default compressed plots are enabled.
--pimHost no no Pim host to publish status to
--pimRunId no no Pim run Id to publish status to
--pimDeleteIfExist no no Delete run if it already exists
--pimFullGraph no no Compress nodes to publish to PIM


PipelineStatus is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


The source code of PipelineStatus can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

PipelineStatus is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on PipelineStatus. We have had good results with this IDE.


For any question related to PipelineStatus, please use the github issue tracker or contact the SASC team directly at: