Command usage:
==============

SyQADA expects the directory in which it is invoked to be the
working directory of a project, `not` the `bin` directory in which the
executable sits.  Exceptions to this are *syqada --help*, *syqada
--version*, and *syqada manual*, which will bring up the manual in a
browser regardless of your current working directory.

SyQADA is constructed as a collection of modules called by a single
driver. The following sub-commands may be used as the first argument to
the syqada command. This first list of sub-commands does not require
a batch directory as an argument.

.. hlist::
   :columns: 2

   * :ref:`syqada_begin`: Start a project using an existing protocol.
   * :ref:`syqada_manual`: Open the manual in a browser.
   * :ref:`syqada_validate`: Test a template, task, or protocol for syntax and parameter substitution.
   * :ref:`syqada_help`: Print help.
   * :ref:`syqada_init`: Prepare the job scripts for the next unfinished task.
   * :ref:`syqada_auto`: Examine the project and run it if there are no errors.
   * :ref:`syqada_status`: Examine the project and report its status.
   * --version: Report syqada version
   * --help:  Print help. --help --help opens the manual.

The sub-commands in the second list require the name of a batch
directory as the second argument.

.. hlist::
   :columns: 2

   * :ref:`syqada_batch`: Build a task directory, write the job scripts, and run them.
   * :ref:`syqada_manage`: Examine a task directory
   * :ref:`syqada_fix`: Examine a task directory and correct mishandled jobs and logs.
   * :ref:`syqada_reset`: Clean up a task directory so that it is ready to initialize from metadata.
   * :ref:`syqada_purge`: Altogether remove a task directory so that it can be entirely recreated.
   * :ref:`syqada_repend`: Move failed jobs to PENDING and clean up their logs from the LOGS directory.
   * :ref:`syqada_errors`: Report errors on a task directory.
   * :ref:`syqada_stderr`: Report a standard error output for jobs in a task directory.  
   * :ref:`syqada_stdout`: Report a standard output for jobs in a task directory.  

In both lists, each subcommand takes additional parameters identified by two leading dashes.
Distinct prefixes of the parameter names are acceptable, for example::

 syqada batch 01-step-one --step initialize

and::

 syqada batch 01-step-one --step init

have identical effect.

Command Index
=============

.. toctree::
   :maxdepth: 2

   syqada_auto
   syqada_batch
   syqada_begin
   syqada_describe
   syqada_enqueue
   syqada_errors
   syqada_fix
   syqada_help
   syqada_init
   syqada_manage
   syqada_manual
   syqada_purge
   syqada_repend
   syqada_reset
   syqada_status
   syqada_stderr
   syqada_stdout
   syqada_validate