This documentation refers to program version $Rev: 371 $
batch_game2gff.pl -i InDir -o OutDir
--indir # Path to the input directory
--outdir # Path to the output directory
This is what the program does
Path to the directory that contains the game.xml files to be converted
from game.xml format to gff format.
Path to the output directory where the GFF format files will be saved to.
The path to the local installation of the Apollo Genome Annotation program.
This can also be defined with the GP_APOLLO_BIN environment variable as
discussed in the CONFIGURATION AND ENVIRONMENT section of the
batch_game2gff.pl program manual.
Short overview of how to use program from command line.
Show program usage with summary of options.
Show program version.
Show the full program manual. This uses the perldoc command to print the
POD documentation for the program.
Run the program with minimal output.
Run the program in verbose mode. This produces the maximum amount
of program status information and can be useful for diagnosing problems.
Error messages generated by this program and possible solutions are listed
- ERROR: No game.xml files were found in the input directory
The input directory does not appear to contain game.xml files.
This could happen because you gave an incorrect path or because your annotation
files do not have the expected *.game.xml extension in the file name.
- ERROR: Could not create the output directory
The output directory could not be created at the path you specified.
This could be do to the fact that the directory that you are trying
to place your base directory in does not exist, or because you do not
have write permission to the directory you want to place your file in.
This program does not require external configuration files but it can make
use of variables defined in the user's environment:
This is the path to the Apollo binary file. This can also be defined at
the command line by the --ap-path variable.
An example of setting the Apollo binary variable in the bash shell is:
This module is required to copy the BLAST results.
This module is required to accept options at the command line.
- Apollo GUI Required
Despite using the command line syntax for Apollo to conver the game files
to xml, this program requires that you have GUI access to the Apollo program.
The batch_game2gff.pl program is part of the DAWG-PAWS package of genome
annotation programs. See the DAWG-PAWS web page
( http://dawgpaws.sourceforge.net/ )
or the Sourceforge project page
( http://sourceforge.net/projects/dawgpaws )
for additional information about this package.
GNU General Public License, Version 3
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED
WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
VERSION: $Rev: 371 $