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:
cmdline.sh - for systems with
a bash-shell (e.g. Linux)cmdline.bat - for Microsoft
Windows Systems
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 cmdline.sh
script for bash shells. Windows users simply replace this command with cmdline.bat.
Example:
cmdline.sh -h - Displays the usage with a complete list of possible flags.
Memory
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:
cmdline.sh -Xmx2048m ... - starts the commandline tool with 2GB of available memory
Tools
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.
- loading data - how to load your data from a file, filter and evaluate it.
- normalization - parameters used for normalization of the data.
- half-life calculation - a description of flags used for half-life
calculation and related methods.