QuickStart

To start ACEseq download package from here and install the reference files and conda package as described under Installation & Run instructions.

sh $PATH_TO_PLUGIN_DIRECTORY/Roddy/roddy.sh \
    rerun \
    ACEseq@copyNumberEstimation \
    $pid \
    --useconfig=$PATH_TO_PLUGIN_DIRECTORY/applicationProperties.ini \
    --cvalues="bamfile_list:$pathToControlBamFile;$pathToTumorBamFile,sample_list:control;tumor,possibleControlSampleNamePrefixes:control,possibleTumorSampleNamePrefixes:tumor"

Following parameters should be changed in the project.xml:

• baseDirectoryReference
• outputBaseDirectory
• outputFileGroup (in case all outputfiles should have different group than primary group)

Alternative running modes:

• runWithoutControl/isNoControlWorkflow (in case it should be run without control)
• runWithFakeControl (in case the coverage should be taken from a different control)