| batch_eugene.pl |
batch_eugene.pl - Run EuGene gene prediction in batch mode
This documentation refers to program version $Rev: 552 $
batch_eugene.pl -i InDir -o OutDir
--indir # Path to the input directory
--outdir # Path to the output directory
This script runs the EuGene gene annotation program in batch mode on a directory of FASTA files.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
Path to the binary for the eugene program. This file should be named eugene. If this path is not supplied at the command line, the program assumes that the directory containing this program is listed in the user's PATH environment variable.
Path to the program egn_getsites4eugene.pl. If this path is not supplied at the command line, the program assumes that the directory containing this program is listed in the user's PATH environment variable.
Path to the parameter file to use. If this path is not supplied at the command line, the program will use the hex_eugene.par file and will assume that the directory cotaining this file is listed in the user's PATH evnironment variable.
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 maximum output.
Run the program with minimal output.
Run the program without doing the system commands. This will test for the existence of input files.
Error messages generated by this program and possible solutions are listed below.
The input directory does not contain fasta files in the expected format. This could happen because you gave an incorrect path or because your sequence files do not have the expected *.fasta extension in the file name.
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 make use of a configuartion file. Instead a eugene specific parameter file must be set with the --param option.
This program does not make use of variables in the user environment.
The batch_eugene.pl program requires that you have a local installation of the EuGene gene annotation program. This program is available from: http://www.inra.fr/internet/Departements/MIA/T/EuGene/
This module is required to accept options at the command line.
Any known bugs and limitations will be listed here.
If you find a bug with this software, file a bug report on the DAWG-PAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
This program has been tested and known to work with EuGene rel 3.3.
The 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.
A manuscript is being submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program:
JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes. http://dawgpaws.sourceforge.net/
GNU General Public License, Version 3
http://www.gnu.org/licenses/gpl.html
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
STARTED: 11/07/2008
UPDATED: 01/20/2009
VERSION: $Rev: 552 $
| batch_eugene.pl |