This guide will show you how to setup Roddy, so that it is starting and ready to run an analysis for a project. There is a sample NGS workflow available, which will be used in the examples.

For a short overview about Roddy usage navigate to Cheat sheet.

If you do not already have a running installation, please see Installation guide for instructions to install Roddy.

After installing Roddy, please head to the Roddy folder and run the Roddy start script:

bash roddy.sh

If everything is good, Roddy will start and print the help.

Roddy is supposed to be a rapid development and management platform for cluster based workflows.
The currently supported ways of execution are:
 - job submission using qsub with PBS or SGE
 - monolithic, direct execution of jobs via Roddy
 - submission or execution on the local machine or via SSH

  To support you with your workflows, Roddy offers you several options:

        Shows a list of available configuration files in all configured paths.


    --usePluginVersion=(...,...)    - Supply a list of used plugins and versions.

Roddy version 2.2.78 build at Fri Sep 18 13:55:26 CEST 2015

Now you can go on and prepare the configuration for your project.

Setup Roddy Configuration

You need two types of configurations:

  1. Application configuration file (by default applicationProperties.ini): A ini formatted file that configures properties of the Roddy application, the batch processing system (PBS, SGE, etc.), default paths for configutations and plugins, etc.
  2. An XML configuration file for your project with all parameters of the workflow that you want to use.

Application ini file

Roddy uses an ini file to control the application behaviour. The ini file define several things:

  • Which job system you use
  • How you connect to the processing system
  • Where Roddy shall search for plugins and configuration files

By default, Roddy will use the ini file located at $HOME/.roddy/applicationProperties.ini, but you can select any other file with the _–useconfig__ command-line option.

The ini files are explained in detail in Application properties files. Here you’ll see a brief overview:


commandLogTruncate=80                       # Truncate logged commands to this length. If <= 0, then no truncation.


The file is divided into several sections, but this is mainly to keep a better order:

  • COMMON is for setting up general things
  • COMMANDLINE is to set up the command line interface

We try to keep every possible option in the ini file, so you should basically be able to just select what you need and to fill in the missing parts.

Usually, you just need to change the following settings:

  • jobManagerClass - Selects the cluster system backend
  • CLI.executionServiceClass - Selects, if you want to access your system via SSH or directly
  • CLI.executionServiceAuth - keyfile or password?
  • CLI.executionServiceHost - The host, if you select SSH
  • CLI.executionServicePasswd - The password for your system, if using SSH and no keyfiles
  • CLI.executionServiceStorePassword - If you want to store the password, put in true, however, the password is stored in plain-text!
  • scratchBaseDirectory - A path to a preferably fast local storage on the execution hosts. E.g. /local/$USER

You might remember or store away the above options for future usage as its likely, that they won’t change too often. For you the more important settings might be:

  • configurationDirectories - Put in a comma separated list of directories, where you keep your project XML files
  • pluginDirectories - Put in a comma separated list of the directories, where your plugins are stored. Note, that the folder dist/plugins in the Roddy base directory, which contains the PluginBase and DefaultPlugin, will always be imported. You do not need to set this one.

You can either copy the content from above or you can also use Roddy to help you with the setup. This will be explained later on.

Project configuration files

All workflow-specific settings are stored in XML files.

The configuration files are multi-level, which means, you can - Import configuration files into other configuration files - Define several level of configurations and subconfigurations in one file

<configuration configurationType='project'
         description='A very small project configuration for some workflow tests.'
        <analysis id='testWorkflow' configuration='TestAnalysis' useplugin="DefaultPlugin:develop"/>
        <analysis id='qualityControl' configuration='QualityControlAnalysis' useplugin="QualityControlPlugin:1.0.10"/>
        <cvalue name='inputBaseDirectory' value='$USERHOME/roddyTests/${projectName}/data' type='path'/>
        <cvalue name='outputBaseDirectory' value='$USERHOME/roddyTests/${projectName}/results' type='path'/>
        <configuration name="verysmall" usedresourcessize="xs" inheritAnalyses="true" />

You as a user normally should only need to create a project specific file like the one above. Roddy also offers a command for you to help you to set this one up.

Configuration files contain several sections where Roddy lets you define things like configuration values, tools and even filenames. But, you probably won’t need that now and we’ll concentrate on a very basic project configuration like the one above. You can find an in-detail guide here XML configuration files. You might concentrate on the configuration values part as this will be the part which you probably need most.

//Uhhh, ok, so what is in the above example?//

Good that you ask! First you’ll find a standard XML format containing the configuration header. If it is a project configuration file (you could e.g. create a file which contains basic settings for your working environment like e.g. commonly used binaries and reference files) then your file must be named with the prefix “projects”. Otherwise it will not be recognized as a project configuration by Roddy.

<configuration configurationType='project'
                     description='A very small project configuration for some workflow tests.'

The header of the configuration must contain the following:

  • The configurationType (in this case “project”)
  • A configuration name which must not contain “.” and ” “

It may contain:

  • A description
  • Imports for other configuration files. import can hold a comma separated list of other configuration id’s / names
  • A switch for the size of the data you are dealing with. In the analysis configuration every tool can have different level of resources im memory, CPU, and walltime. This option in the project XML allows you to select a project-wide resource requirement level for the size of the input data expected in the project. The values t, xs, s, m, l, xl are allowed the and default is “l”.

Directly after the header, you will find a list of the imported workflows for your project.

    <analysis id='testWorkflow' configuration='TestAnalysis' useplugin="DefaultPlugin:develop"/>
    <analysis id='qualityControl' configuration='QualityControlAnalysis' useplugin="QualityControlPlugin:1.0.10"/>

Each line can enable a workflow / analysis for your project. To make such a line work, you need to set:

  • id an arbitrary name that identifies the workflow in your project. This name will be used to call the workflow from the command line.
  • configuration to identify the original analysis configuration id that is defined in the analysis XML in the plugin. You can also import an analysis several times with a different id value.
  • finally, useplugin is used to select the plugin and the plugins version, in which the analysis is searched. This parameter is optional.

The corresponding configuration files are automatically searched in your plugins. The active plugins are retrieved from the plugin directories set in you application ini file.

Next comes the part where you set the projects input and output folder.

    <cvalue name='inputBaseDirectory' value='$USERHOME/roddyTests/${projectName}/data' type='path'/>
    <cvalue name='outputBaseDirectory' value='$USERHOME/roddyTests/${projectName}/results' type='path'/>

In most cases, you should be done right now.

Analysis-specific configuration

Occasionally, you may want to set specific parameters only for selected analyses. In this case you can add subconfigurations:

    <configuration name="verysmall" usedresourcessize="xs" inheritAnalyses="true" />

Subconfigurations are exactly defined like the main configuration. They can contain the same sections. Each value, which is defined by you, overrides a value of the parent configuration. Subconfigurations can be nested and affect all ** tags that are nested within.

Built-in configuration creation / updates

Use Roddy to create an initial project configuration

Roddy can help you to create an initial project configuration with one command.

bash roddy.sh prepareprojectconfig create [targetprojectfolder] --useRoddyVersion=develop

The command will:

  1. Create a target folder structure like [targetprojectfolder]/roddyProject/versions/version_[current date]_[current time]
  2. Copy a default ini file to the target folder [targetprojectfolder]/applicationProperties.ini
  3. Copy a default project XML to the target folder [targetprojectfolder]/project.xml

You can now update both the ini file and the XML file to your needs. Do not forget to place the freshly create folder as a configuration folder to the ini file! Please see the explanation above to decide which settings are appropriate for your system.

To use the ini file, you can call Roddy in the following way:

bash roddy.sh --useconfig=[targetprojectfolder]/applicationProperties.ini

Use Roddy to update an existing project configuration to a new version

Sometimes it is helpful to keep several version for project configuration files. This ensures, that you can always try to go back to an old version of your config. To support this, you can call Roddy in the following way:

bash roddy.sh prepareprojectconfig update [targetprojectfolder]

Roddy will then search the latest existing project configuration version and create a new folder with a copy in it.

So after you call Roddy, you’ll find e.g.:

  • [targetprojectfolder]/roddyProject/versions/version_20150719_111328 and
  • [targetprojectfolder]/roddyProject/versions/version_20150925_134527

The new folder will contain a copy of the contents of the old folder. You can call Roddy afterwards with the new ini file.

IMPORTANT: Roddy does not update the configurationDirectories option in the new applicationProperties.ini. As of now, you need to manually adapt the configuration directories in the ini file!

Check if things are set up properly

With configurations of complex workflows, it may become very tedious and error prone to ensure that everything is configured correctly. If you work with multiple projects, the first thing to check is the use of the correct configuration files. To find out, if you did everything right, Roddy offers you several options:

bash roddy.sh showconfigpaths  --useconfig=[pathOfIniFile]

This will show you all available configuration files in your configured paths. Note, that this won’t list analysis XML files, as these are loaded in a later stage, where Roddy has knowledge about loaded plugins.

With the following command you can check, whether you set the right paths and if all your files are available:

bash roddy.sh listdatasets [project]@[analysis] --useconfig=[pathOfIniFile]


Roddy supports parsing metadata such as dataset identifiers from paths but additionally has a MetadataTable facility that simplifies metadata input via a table. Some workflows may also be implemented to get the metadata from dedicated configuration values. Therefore, whether this command works may depend on the specific workflow and may require additional command-line parameters or configuration values. Still it can be extremely useful to get a list of all findable datasets.

If everything is properly set and you use the right configuration and analysis, Roddy will be able to search the input and output folders in your project configuration file. It will then display a list of all found datasets. Roddy will search both folders and the result will be combined, so you will not get doublettes. If you see the list of your datasets, you can now run your analysis, but before you do this, you can also try some more things before.

bash roddy.sh printruntimeconfig [project]@[analysis] [pid] --useconfig=[pathOfIniFile]

If you run a workflow for the first time, it might make sense to check the generated runtime configuration file before you start a process. The above command will do that for the pid set by you. Is everything right? Good, then you can go on and start a process. If not, you need to check your configuration files.

Run a project

There is one more thing you can do before starting a process: You can call Roddy with testrun:

bash roddy.sh testrun [project]@[analysis] [pattern]/[ALL] --useconfig=[pathOfIniFile]

testrun will nearly do the same thing as run, except, that it does not start cluster jobs. It will list all the jobs which will be executed. Please take a close look at the output for all the jobs. testrun and all the other run commands are all triggered with a dataset id pattern. We’ll explain that soon.

Some explanation for the dataset patterns. Roddy selects and lists datasets like e.g. ls. This means, you can use all sorts of wildcards and patterns. Valid patterns are e.g. H063, *-A*, ???3- and so on. But! Keep in mind, that wildcards will may already be resolved by the shell (e.g. Bash is always good for surprises). testrun will help you find out, if the patterns you use are working. Also note, that a plain * won’t work at least for Bash. If you want to run all datasets, use the dataset selector [ALL].

Now let’s look at an example for a job output:

0x789C44FF73F: fastqc [ -l walltime=1000:00:00]
  pid                       : H006-1
  PID                       : H006-1
  CONFIG_FILE               : [ exDir]/runtimeConfig.sh
  ANALYSIS_DIR              : /home/heinold/temp/roddyLocalTest/testproject
  TOOLSDIR                  : [ exDir]/analysisTools/qcPipeline
  TOOL_ID                   : fastqc
  RAW_SEQ                   : [ inDir]/control/paired/run120918_SN7001149_0101_AC16PKACXX/sequence/1_B_GCCAAT_L002_R1_complete_filtered.fastq.gz
  FILENAME_FASTQC           : [outDir]/fastx_qc/control_run120918_SN7001149_0101_AC16PKACXX_1_B_GCCAAT_L002_R1_sequence_fastqc.zip
  RODDY_PARENT_JOBS         : parameterArray=()

This is the output for a job calling fastqc on a fastq file, to go easy, we just named it fastqc. First, there is a fake job id, which is used in test cases. If you call run instead of testrun, this will be replaced by a job identifier produced by your processing backend (PBS, SGE, etc.). The job id is followed by the resource settings specific to your configured processing backend. Here it is the walltime setting for a PBS system. The next lines are the parameters which will be passed to the job. Some of the parameters are set for every job including pid/PID (“patient id”, this is the “dataset”), CONFIG_FILE or ANALYSIS_DIR. The abbreviations like [exDir] or [inDir] are explained in the header of the testrun output. They are there to make things more readable. Other parameters like e.g. FILENAME_FASTQC are job specific. In this case, there is a fastq file for the job input and a zip file containing the job output. Filenames are based on rules which are normally included in analysis configuration files.

Let’s see, showconfigpaths worked, listdatasets worked, printanalysisxml worked and also testrun. What’s left? Right: run!

Let’s start and run something.

bash roddy.sh run [project]@[analysis] [pattern]/[ALL] --useconfig=[pathOfIniFile]

Instead of the output of testrun, Roddy will now try and run the jobs on your processing backend. If all jobs fail, you might have the wrong settings. If some fail, there might be problems with the backend. Roddy will also try to tell you what sort of problems there are. But this won’t work in every case. We won’t bother you with the full output now, but something like the following will show up in case of success:

Finally, you started something. Now all you have to to is to wait until your process finishes. Roddy will again offer you several commands to help you keep track of your progress.

Process tracking, Debugging and Rerunning a process

Sometimes, it can be nice to know if a process is still running or if there were faulty jobs and sometimes you just want to restart a process. Roddy has what you need: checkworkflowstatus, testrerun and rerun.

bash roddy.sh checkworkflowstatus [project]@[analysis] [pattern]/[ALL] --useconfig=[pathOfIniFile]

checkworkflowstatus will create a table listing your selection of datasets and their states:

[outDir]: /home/heinold/temp/roddyLocalTest/testproject/rpp
Dataset       State     #    OK   ERR  User      Folder / Message
A100          UNSTARTED 0    0    0    Not executed (or the Roddy log files were deleted).
A200          UNSTARTED 0    0    0    Not executed (or the Roddy log files were deleted).
stds          OK        3    3    0    testuser   /home/testuser/temp/roddyLocalTest/testproject...

The table has several columns:

  • Dataset is self explaining and shows you for which dataset the line is
  • State is the state for the last execution of a dataset
  • Is the number of started jobs for a process ===========================================
  • OK is the number of good jobs
  • ERR is the number of faulty jobs
  • User is the user which started the last process
  • Folder / Message is the execution store folder for the process

You can e.g. use the output to grep for states, folders and other things. If there are errornous jobs, you now have the info to look for those jobs. The next section will show you, how to do this. For know, we’ll consider the jobs as failed for technical reasons and show you how to restart them.

Roddys restart / rerun option tries to start only jobs which need to be run. For this, it creates a list of all the output files which it knows and compares these files with the existing files on disk. There are no consistency checks done, so files with the size of zero are also taken into account. If a job has failed, all of its descendants are automatically marked as failed. This is also true, when a new job will get startet. What the workflow then does is within the responsibility of the workflows author. Similar to testrun / run, testrerun and rerun will start to process data. However, only necessary jobs will be started.

Import list for different workflows:

Please consider using only one analysis import per project XML file, if you set configuration variables. Configuration values for different workflows might have the same name, which could lead to misconfigured workflows. If you do not want to create a new file for every analysis, you can still use subconfigurations for the different workflows using the configuration attribute of the analysis tag:

<!-- Roddy 2.2.x -->
<analysis id='snvCalling' configuration='snvCallingAnalysis' useplugin="COWorkflows:1.0.132-4" />
<analysis id='indelCalling' configuration='indelCallingAnalysis'  useplugin="COWorkflows:1.0.132-4" />
<analysis id='copyNumberEstimation' configuration='copyNumberEstimationAnalysis' useplugin="CopyNumberEstimationWorkflow:1.0.189" />
<analysis id='delly' configuration='dellyAnalysis' useplugin="DellyWorkflow:0.1.12"/>

<!-- Roddy 2.3.x -->
<analysis id='WES' configuration='exomeAnalysis' useplugin="AlignmentAndQCWorkflows:1.1.39" />
<analysis id='WGS' configuration='qcAnalysis' useplugin="AlignmentAndQCWorkflows:1.1.39" />
<analysis id='postMergeQC' configuration='postMergeQCAnalysis' useplugin="AlignmentAndQCWorkflows:1.1.39"/>
<analysis id='postMergeExomeQC' configuration='postMergeExomeQCAnalysis' useplugin="AlignmentAndQCWorkflows:1.1.39"/>

<!-- Roddy 3 -->
<analysis id='rdw' configuration='snvRecurrenceDetectionAnalysis' useplugin="SNVRecurrenceDetectionWorkflow"/>
<analysis id='WGBS' configuration='bisulfiteCoreAnalysis' useplugin="AlignmentAndQCWorkflows:1.1.39"/>