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Running MXP: Command Line

`mxp-init`

Each analysis directory must be initialized before MXP work can be started. Initialization includes creating subdirectory mxp and file mxp.conf inside it. File mxp.conf specifies name of the dataset being analyzed (some methods may use this name) and parent pipeline. Parent pipeline may be specified either as path to mxp subdirectory of the parent, or by giving the name of the parent. In the later case, Bash script named export_ParentPipelineName.sh must exist somewhere in the PATH.

The script mxp-init performs this work.

Usage:

mxp-init [options] directory-to-initialize

Possible options are:

-h, --help: Print help message and exit.
-f, --force: Forces deleting existing mxp.conf file.
-n, --parent-name PLNAME: Name of the parent pipeline. Defaults to basename of PLDIR if PLDIR is specified, or to MXP otherwise.
-p, --parent-dir PLDIR: Directory of the parent pipeline. No default; PLDIR is not set if this option is not given.
-d, --dataset DSNAME: Dataset name. Defaults to basename of the directory to initialize.

If both PLNAME and PLDIR are given, the parent pipeline is determined by PLDIR; PLNAME is used only for messages.

`mxp`

This is the main script that performs the work.

Usage:

mxp [options] target

Possible options are:

-h, --help: Print help message and exit.
-V, --version: Print MXP version and exit.
-m, --maindir ANDIR: Path to analysis directory. Defaults to the current directory.
-w, --width WIDTH: The expandable output strings will use WIDTH columns. Defaults to the current width of terminal window minus 2.
-f, --force-delete: Forces deleting result directory if it exists but is not current.
-n, --dry-run: Do not do anything, just print what would be done.
-v, --verbose: Print more info. Multiple -v options may be specified to further increase verbosity. Currently, up to two -v options are implemented.
-l, --log: Create log file of the current run. If give, file named mxp_target_timestamp.log containing all terminal output will be created. This option is rarely needed, as the log of obtaining target is always written to target-dir/.mxp directory.