Command line options

Following are some of the available options for invoking smrtpipe.py:

-D key=value

• Overrides a configuration variable. Configuration variables are key-value pairs that are read from the global file smrtpipe.rc before starting an analysis. An example is the NPROC variable which controls the number of simultaneous processors to use during the analysis. To restrict SMRT Pipe to 4 processors, use -D NPROC=4.

--debug

• Activates debugging output in the stderr and log outputs. To set this flag as a default, specify DEBUG=True in the smrtpipe.rc file.

--distribute

• Distributes the computation across a compute cluster. For information on onfiguring SMRT Pipe for a distributed computation environment, see SMRT Analysis Software Installation. (Add link)

--help

• Displays information about command-line usage and options, and then exits.

--noreports

• Turns off the production of XML/HTML/PNG reports.

--nohtml

• Turns off the conversion of XML reports into HTML. (This conversion requires that Java be installed.)

--output=outputDir

• Specifies a root directory to use for all SMRT Pipe outputs for this analysis. SMRT Pipe places outputs in this directory, as well as in data, results, and log subdirectories.

params=params.xml

• Specifies a settings XML file for running the pipeline analysis. If this option is not specified, SMRT Pipe prints a message and then exits.

--totalCells

• Specifies that if the number of cells in the job is less than totalCells, the job is not marked complete when it finishes. Data from additional cells will be appended to the outputs, until the number of cells reaches totalCells.

--recover

• Attempts to rerun a SMRT Pipe analysis starting from the last successful stage. The same initial arguments should be specified in this case.

--version

• Displays the version number of SMRT Pipe and then exits.

--kill

• Kills a SMRT Pipe job running in the current directory. This works with output.