Using the command line

In a typical SMRT Analysis installation, SMRT Pipe is in your path after sourcing the setup.sh file. To do so, enter the following:

. /opt/smrtanalysis/etc/setup.sh

Note: Make sure to replace /opt/smrtanalysis with the path to your SMRT Analysis installation.

To check that SMRT Pipe is available, enter the following:

smrtpipe.py --help

This displays a help message describing how to run smrtpipe.py and all of the available command-line options.

You invoke SMRT Pipe with the following command:

smrtpipe.py [--help] [options] --params=settings.xml xml:inputFile

Logging messages are printed to stderr as well as a log file (log/smrtpipe.log). It is standard practice to pipe the stderr messages to a file using redirection in your shell, for example appending &> smrtpipe.err to the command line if running under bash.