set <parameter name> <value>

    Sets the value of a parameter to a given value.  The following parameter

    are available.  Run 'help set <parameter name>' for more detailed

    information.

    verbose     Sets the verbose mode.

    onErrors    Sets the behavior of the interpreter when errors are

                    encountered.

    currDir     Sets the current directory.

    outputFileOverwritePolicy

                Sets the file overwrite policy.

    set verbose <"true" or "false">

    Sets the value of the 'verbose' parameter.  If the 'verbose' parameter is

    set to 'true', extra information is provided about the commands that are

    executed.  This may be useful to help debug scripts.

    set onErrors <"stop" or "continue">

    Sets the value of the 'onErrors' parameter.  If 'onErrors' is set to

    'stop', the command interpreter will stop the current running script

    if an error is encountered.  If 'onErrors' is set to 'continue', the

    command interpreter will abort the command that caused the error but

    will continue running and executing subsequent commands.  

    In the case that the interpreter stops due to an error, if it is running

    a "top level" script (i.e., one that was not started from another script

    with 'utility execute'), then the command interpreter will exit.  If the

    running script was started from another script using the 'utility execute'

    command, then control will be returned to the calling script and the 

    'utility execute' command in the calling script will be treated as if it

    encountered an error.  The behavior in the calling script then depends on

    how the 'onErrors' parameter is set in its environment.  If set to 

    'continue', the calling script will continue running the commands

    subsequent to the 'utility execute'; otherwise, it will stop the calling

    script:  this same rule is applied again in the case that the calling

    script was itself invoked via a 'utility execute' from another script.

    Run 'help utility execute' for information about how one script can execute

    another script.

    set currDir <path>

    Sets the current directory used to resolve relative file paths.  If the

    indicated path does not exist or is not a directory, a warning is shown.

    Run 'help general filePaths' for more information about file paths.

    set outputFileOverwritePolicy <"allow", "warn", or "error">

    Sets the value of the 'outputFileOverwritePolicy' parameter, which

    determines what should happen when a command attempts to overwrite

    a preexisting file.  When set to "allow" (the default), preexisting files

    are silently overwritten.  When set to "warn", such files are also

    overwritten, but a warning message is issued.  When set to "error",

    an error message will be displayed and the command attempting to perform

    the file overwrite will immediately be stopped.

    This policy affects all commands that produce output, such as would be

    generated using the '-outputFile' option of the various 'list' and 'report'

    commands, as well as might be output using automatically generated file

    names by the 'report alignment' command.  The policy additionally affects

    the '-outputFile' and '-scriptOnly' options of 

    'utility makeSetupScript' and 'utility clone' commands, respectively.

    This policy is not relevant to the internal files that are used to store a

    project.  Thus, regardless of the 'outputFileOverwritePolicy', neither the

    'create project' nor the 'utility clone' commands will let you overwrite a

    preexisting project directory.  Similarly, there are no errors or warnings

    involved when using the 'save' command to update an existing project or

    when updating the internal files of a project to store results when the

    'computation start' command is given.

    Run 'help set onErrors' for information about how errors are handled within

    an executed script.  

© 2011 454 Life Sciences Corporation, a Roche Company.

For life science research only. Not for use in diagnostic procedures.