The project configuration "ACEseq" could not be found (call Roddy with listworkflows)

[ccchen-ccc]

Sorry, I dont know how to add the project into Roddy as the applicationProperties.ini has been set

[vinjana]

If a project configuration is not found by Roddy this can have multiple reasons

1. Typo in the configuration name. The name in the name attribute of the (top-level) and the names in the subconfigurations must match exactly what you request the CLI. Subconfigurations are separated by ..
2. The project configuration XML is not in any of the directories searched in by Roddy. There could be a typo on the configurationDirectories variable in your applicationProperties.ini or the value to the --configurationDirectories CLI parameter. Multiple directories should not be separated by spaces but only by commata.
3. The project XML may not be accessible due to missing permissions.

Can you check these things?

[ccchen-ccc]

I have checked your advice and still gain this error below.This is my erro:

(ACEseqWorkflow) [ccc@cccv2-54b47d48b8-9jdct Roddy]$ ./roddy.sh run ACEseq@copyNumberEstimation test --useconfig=/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/configuration/applicationProperties.ini
Required JRE/JDK: 1.8
Required Groovy: 2.4
Runtime Environment:
/home/anaconda2/bin/java
/home/anaconda2/bin/javac
/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/runtimeDevel/groovy-2.4.7/bin/groovy
Using Java to start Roddy
Roddy version 2.4.10
Loading properties file /data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/configuration/applicationProperties.ini.
The project configuration "ACEseq" could not be found (call Roddy with listworkflows)
Could not load analysis ACEseq@copyNumberEstimation

my projectACEseq.xml:

<cvalue name="baseDirectoryReference" value="$HOME/data_soft/PreparedRoddyZip/reference/hg19_GRCh37_1000genomes/" type="path"/>
<cvalue name='inputBaseDirectory' value='$HOME/test' type='path'/>
<cvalue name='outputBaseDirectory'  value='$HOME/test/output' type='path'/>
<cvalue name='outputAnalysisBaseDirectory' value='${outputBaseDirectory}/${pid}' type='path'/>

[ccchen-ccc]

<configuration configurationType='project' name='ACEseq' description=''>

<availableAnalyses>
<analysis id="copyNumberEstimation" configuration="copyNumberEstimationAnalysis" useplugin="ACEseqWorkflow:1.2.10"/>
</availableAnalyses>

<configurationvalues>
<cvalue name="workflowEnvironmentScript" value="${TOOL_WORKFLOW_ENVIRONMENT_CONDA}" type="string"/>
<cvalue name="condaEnvironmentName" value="ACEseqWorkflow" type="string" description="Name of the Conda environment on the execution hosts. Used by the environment setup script in resources/analysisTools/copyNumberEstimation/enviroments."/>

<cvalue name="baseDirectoryReference" value="$HOME/data_soft/PreparedRoddyZip/reference/hg19_GRCh37_1000genomes/" type="path"/>
<cvalue name='inputBaseDirectory' value='$HOME/test' type='path'/>
<cvalue name='outputBaseDirectory' value='$HOME/test/output' type='path'/>
<cvalue name='outputAnalysisBaseDirectory' value='${outputBaseDirectory}/${pid}' type='path'/>

</configuration>
`

[vinjana]

Dear @ccchen-ccc . First I see that you use Roddy 2.4. I strongly advise you to use the newest available Roddy version, because there are a lot of bug-fixes and UI-improvements, such as better error-reporting and reporting of directories being used. Furthermore, I remember that we made a plugin-version bump from the 1.0 versions to 1.2 versions to express the fact, that the newer versions work only with Roddy 3.

Your project XML misses the closing </configurationvalues> tag. Please use the very latest Roddy version to ensure that such error is actually resulting in an exit code != 0 (a bug that was just fixed last week). Your specification ACEseq@copyNumberEstimation seems to be fine.

Beyond that, the only reason I can think of in the moment are really that Roddy cannot access the file. The project XML needs to be in a directory listed among the configurationDirectories. So, Roddy will also not search the current/working/execution directory. Furthermore make sure to always and everywhere use absolute paths.

[ccchen-ccc]

Thank you !!! Error happened when i used relative path in the file ini. Sorry disturbing you again, i don't understand what's the meaning of 'dataset' when starting Roddy. Here is my problem:

root@ccc950-79cfd9f9fd-4jjtl:/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy# ./roddy.sh testrun ACEseq@copyNumberEstimation $pid --useconfig=$PATH_TO_PLUGIN_DIRECTORY/configuration/applicationProperties.ini --cvalues="bamfile_list:$pathToControlBamFile;$pathToTumorBamFile,sample_list:control;tumor,possibleControlSampleNamePrefixes:control,possibleTumorSampleNamePrefixes:tumor"Required JRE/JDK: 1.8
Required Groovy: 2.4
Runtime Environment:
/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/runtimeDevel/jdk1.8.0_121/bin/java
/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/runtimeDevel/jdk1.8.0_121/bin/javac
/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/runtimeDevel/groovy-2.4.7/bin/groovy
Using Java to start Roddy
Roddy version 2.4.10
Loading properties file /data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/configuration/applicationProperties.ini.
Ignore directory /data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/plugins/PluginBase_1.2.0/resources/analysisTools/.keep; It is not a valid tools directory.
The plugin ACEseqWorkflow [ Version: 1.2.10-0 ] was loaded (/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/plugins/ACEseqWorkflow_1.2.10).
The plugin COWorkflowsBasePlugin [ Version: 1.0.0-0 ] was loaded (/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/plugins/COWorkflowsBasePlugin_1.0.0).
The plugin PluginBase [ Version: 1.2.0-0 ] was loaded (/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/plugins/PluginBase_1.2.0).
The plugin DefaultPlugin [ Version: 1.2.0-0 ] was loaded (/data/user/ccc/ccc_I950/data_soft/PreparedRoddyZip/Roddy/dist/plugins/DefaultPlugin_1.2.0).
BEJob id for de.dkfz.roddy.execution.jobs.direct.synchronousexecution.DirectSynchronousExecutionJobManager should be configurable
BEJob arrays are not supported in de.dkfz.roddy.execution.jobs.direct.synchronousexecution.DirectSynchronousExecutionJobManager
BEJob scratch for de.dkfz.roddy.execution.jobs.direct.synchronousexecution.DirectSynchronousExecutionJobManager should be configurable
Found 1 datasets in the in- and output directories.
The workflow does not seem to be executable for dataset output
Context access rights settings could not be validated.

There were errors for the execution context for dataset output
* The workflow setup is not correct. SEVERE: The requested user group B080 is not available on the target system.
Disable Roddys access rights managemd by setting outputAllowAccessRightsModification to true or
Select a proper group by setting outputFileGroup.
There were no executed jobs for dataset output

Thanks for reply!!

[ccchen-ccc]

What i need to config in the "dataset'?

[vinjana]

"dataset" is basically the patient ID (PID). Practically its the names of the subdirectories of the input or output directories, which is also used in some other filenames.

[ccchen-ccc]

I had create a folder named "output" in the input or output directories, but it showed that 'the workflow does not seem to be executable for dataset output'. I don't know how to config the workflow or what the "dataset" need?

[vinjana]

Some notes:

• ACEseqWorkflow version 1.2.10 is deprecated. Is there a particular reason you are using this version? If not, better switch to 1.2.8-4_LSF.6, which is also currently used executed by the much improved Roddy 3.5 in production at our institute. For Roddy 2, I try to avoid giving support, because all workflows were fully migrated to Roddy 3 and because of the additional maintenance that we cannot stem anymore (for that reason Roddy have been phased out and will not be further developed). A well working stack is: COWorkflowBasePlugin 1.0.2, ACEseqWorkflow 1.2.8-4_LSF.6, Roddy 3.5.7.
• Better set the configuration variable outputAllowAccessRightsModification to false to get rid of the corresponding error. Ideally, the access rights should be managed via the access rights on the input and output directories. The Roddy mechanism turned out to be unreliable. If you still want to use it, follow the instructions and change outputFileGroup to an existing Unix group you are a member of.