runPipeline Options

The following are the list of command line options that can be passed to the runPipeline.sh script. Parameters not set via command line options will be read from a loadParameters.m file in the same directory. This list is also available via the -h option of runPipeline.sh . The possible options are:

Parameter	Description
--configure	This allows for parameters to be set interactively either by a GUI or if there is not an available display, parameters will be set via a command line interface. This option requires python. A more detailed description is available in the below section.
--auto-config	Attempts to automatically set the base name and number of rounds based on the files in the input path.
-I	Sets the input data directory where the initial images are read from.
-O	Sets the output directory; the parent directory containing the directories for each stage. See Input Data Preparation for a description of the containing folders.
-N	The number of rounds in the input data.
-b	The base filename of the input data.
-B	Round number to use as the reference round for registration.
-i	Reporting directory to store images in produced by some of the additional analysis scripts.
-T	Temporary directory to store extra information needed by the color correction and normalization stages.
-L	Log directory which stores any logging information produced including Matlab logs.
-A	Acceleration to use can be either CPU or GPU_CUDA.
-F	File format intermediate images will be stored in can be either tiff or hdf5.
-J	This option allows any parameter other parameter to be set in a comma separated list i.e. A=1,B=2,C=\'c\'.
-P	Profile performance during execution. This option requires more details and has a dedicated wiki page here.
-e	List of specific stages to be run rather than the full pipeline. The list of possible stages are: setup-cluster,color-correction,normalization,registration,puncta-extraction,base-calling. Multiple stages can be specified with this option. It is important to note that with this option the pipeline will still check if output files exist and not re-run processing if they do.
-s	List of stages to skip; all stages apart from the ones listed in this option. Uses same stages as the above -e option.
-y	Automatically answers all interactive prompts with yes. Without this option the pipeline will present what options it is using and will ask the user to confirm. This is useful running the runPipeline.sh script form another wrapper script.
-h	Print a help message showing a quick list of options and what they do.

Configure

This section adds additional information about the command line questions offered by the --configure option.

The command line options are asked in order:

1. File path to directory containing input images (same as -I option).
2. Basename of the input files. (same as -b option).
3. Channel names to use that; this must be a comma separated list of 4 strings (ExSequence only supports exactly 4 color channels) which are appended on to the basename. By default is ch00,ch01,ch02,ch03 meaning the first round and channel file name is basename_round001_ch00.
4. Path to output directory containing the directories for each stage (same as -O option; see Input Data Preparation).
5. File type to use for input and intermediate files options are 1 for tiff and 2 for hdf5.
6. Path to temporary storage; store additional files for color correction and normalization here (same as -T option).
7. Path for log files (same as -L option).
8. Total number of rounds (same as -N option).
9. Round to use as reference round for registration (same as -B option).
10. Whether to use GPU-CUDA acceleration (1 for yes, 2 for just CPU acceleration).