Configuration file

If atools was installed for you by your friendly local system administrator, you do not have to worry about the log file, it is installed with atools and configured to do the right thing on your system.

The log file is in Python's ConfigParser format, and contains the defaults for the system atools is installed on. The first global section is where these defaults are set.

# batch system to use
batch_system = torque
# default reduce mode
mode = text
# default Linux shell
shell = bash

The supported batch systems are:

  • torque: PBS torque,
  • moab: Adaptive Computing Moab,
  • sge: SUN Grid Engine,
  • slurm: Slurm workload manager.

The supported standard reduction modes are:

  • text: concatenate text files, assuming no header information,
  • csv: concatenate CSV files, assuming the first line contains the column definitions.

The supported shells are:

  • bash: Bourn again shell
  • sh: Bourn shell
  • tcsh: Tennex C shell
  • csh: C shell

The remaining sections of the configuration file should normally not be touched, unless to add additional reduce modes, support for shells or batch systems.