
                                  acdlog 



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Function

   Test application ACD file processing and trace data structures

Description

   acdlog processes an ACD file and user input, while logging the
   contents of internal data structures. For the time being it's use is
   deprecated and the entrails application should be used instead.

   acdlog works the same as acdc but reports on the data structures used
   to process the ACD file.

Usage

   [an error has occurred processing this directive]

Command line arguments

   The first parameter is the name of the program to compile. All other
   command line parameters and qualifiers are defined for that program -
   see the documentation for the program of choice.

Output file format

   The output file of the program being logged is empty, but any format
   available to the specified program can be used.

   The processing output is written to a file with the extension
   ".acdlog"

   [an error has occurred processing this directive]

Data files

   Acdlog will use any data files specified in the ACD file of the
   specified program, but will ignore any data files that are only used
   directly by the program's code.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   acdlog does not have its own options, but takes a single parameter
   which is the name of the EMBOSS application that is being testsed. It
   is invoked by specifying the name of the application to be tested
   along with any command-line options after the name of the utility
   application itself:

   acdlog ApplicationName Options

   acdlog will run the command line interface of any EMBOSS program by
   reading its ACD file and processing the command line and user
   responses in exactly the same way as if the true program itself were
   running. The application proper is not run; it is only the ACD file
   that is read. Any command-line options for the application being
   called can be specified. The user is prompted for any required values
   for application parameters and any input files are read. Output files
   can be specified in any available format however they will be empty
   (the application code is not called so there will be no output).

References

Warnings

   None.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   acdc             Test an application ACD file
   acdpretty        Correctly reformat an application ACD file
   acdtable         Generate an HTML table of parameters from an application ACD
                    file
   acdtrace         Trace processing of an application ACD file (for testing)
   acdvalid         Validate an application ACD file

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

   This program is intended to be used by developers of applications and
   interfaces.

Comments

   None
