atools requires at least Python 2.7.x, but only uses the standard library.

Supported queue systems and schedulers:

  • PBS torque,
  • Moab (Adaptive Computing),
  • SUN Grid Engine,
  • Slurm workload manager.


After downloading a release from GitHub and unpacking, simply run

$ ./configure --prefix=<install-path>
$ make install

Note: atools will be configured to use the Python that is in your PATH when installing. If you change your mind afterwards, edit conf/ to your liking.

Depending on the batch system you use, the --with-batchsystem configure option should be set appropriately, i.e.,

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

The default is torque

One can also specify the default shell atools will assume for job scripts at installation time by using the --with-shell configure option. It defaults to bash, but sh, csh, and tcsh are also accepted. Note that all relevant atools commands have a --shell option which overrides the installation default.

In addition, one can set the default reduce mode as either text or csv using the --with-reducemode configure option. Again, areduce has a --mode option to override this at any time.

Note that a reinstall is not required to change these installation default, you can simply edit the conf/atools.conf file to modify atools behavior after installation.


Ensure that the bin directory is in your path when executing atools commands, i.e., by adding it to the PATH environment variable.

Note that the Python run time dependency is "hidden" within atools configuration, and is only required from within the bash wrapper scripts, so using atools will not pollute any environment variables except PATH.