batch_eugene.pl


NAME

batch_eugene.pl - Run EuGene gene prediction in batch mode


VERSION

This documentation refers to program version $Rev: 552 $


SYNOPSIS

Usage

    batch_eugene.pl -i InDir -o OutDir

Required Arguments

    --indir         # Path to the input directory
    --outdir        # Path to the output directory


DESCRIPTION

This script runs the EuGene gene annotation program in batch mode on a directory of FASTA files.


REQUIRED ARGUMENTS

-i,--indir

Path of the directory containing the sequences to process.

-o,--outdir

Path of the directory to place the program output.


OPTIONS

--eugene-binary

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.

--get-sites

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.

-p,--param

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.

--usage

Short overview of how to use program from command line.

--help

Show program usage with summary of options.

--version

Show program version.

--man

Show the full program manual. This uses the perldoc command to print the POD documentation for the program.

--verbose

Run the program with maximum output.

-q,--quiet

Run the program with minimal output.

--test

Run the program without doing the system commands. This will test for the existence of input files.


DIAGNOSTICS

Error messages generated by this program and possible solutions are listed below.

ERROR: No fasta files were found in the input directory

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.

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.


CONFIGURATION AND ENVIRONMENT

This program does not make use of a configuartion file. Instead a eugene specific parameter file must be set with the --param option.

Environment

This program does not make use of variables in the user environment.


DEPENDENCIES

Required Software

Required Perl Modules


BUGS AND LIMITATIONS

Any known bugs and limitations will be listed here.

Bugs

Limitations


SEE ALSO

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.


REFERENCE

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/


LICENSE

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.


AUTHOR

James C. Estill <JamesEstill at gmail.com>


HISTORY

STARTED: 11/07/2008

UPDATED: 01/20/2009

VERSION: $Rev: 552 $

 batch_eugene.pl