Command line tools

HALO provides a set of command line tools for fast access to the framework of methods for half-life calculation and related analyses. This service can easy be used for automated computations and batch jobs. In this section of the documentation you can find general information on how to use these tools, including descriptions of accessing the command line framework and lists of available methods. For an easier understanding example calls are provided for each function of the tools, and an example use case analogous to those for the GUI and the Java API.

Calling from the command line

All tools are called using a single script file which can be found in the root directory of the package:
The set of parameters passed to the script can be combined individually for a custom output. For a complete list of possible parameters call the script without any parameters, or the flags -h or help. The combinations of flags used as parameters defines, which calculational methods are performed. You can find a more detailed description of these parameters in this section.

Note: All examples in this documentation use the script for bash shells. Windows users simply replace this command with cmdline.bat.

Example: -h - Displays the usage with a complete list of possible flags.


By default 1GB of memory will be available for the Java VM when using a command line tool. If you want to change this amount, specificy -Xmx000m as the first argument where 000 is the amount of megabytes which will be available. (Note: the -Xmx parameter is directly passed to the Java virtual machine, syntax errors will cause error messages of the Java interpreter).

Example: -Xmx2048m ... - starts the commandline tool with 2GB of available memory


The set of command line tools can be divided into the three main parts of the HALO framework: Data filtering, Normalization and Half-life calculation. Which of these is performed is depending on the set of parameters called with the script. For every of the listed methods the previous loading of data is needed; how to do this is described in the first section loading data. Below you can find a detailed description of every of these sections, as well as information on how they are depending on each other.

HALO documentation