QuickStartΒΆ
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 (in case it should be run without control)
- runwithFakeControl (in case the coverage should be taken from a different control)