batch_genemark.pl


VERSION

This documentation refers to batch_genemark.pl version $Rev: 555 $


SYNOPSIS

Usage

    batch_genemark.pl -i DirToProcess -o OutDir

Required Arguments

    -i, --indir    # Directory of fasta files to process
    -o, --outdir   # Path to the base output directory
    -c, --config   # Path to the config file


DESCRIPTION

Run the GeneMarkHMM gene prediction program in batch mode. Runs genmark as well as converts output to gff format. Requires a config file to specify libraries to use.


REQUIRED ARGUMENTS

-i,--indir

Path of the directory containing the sequences to process.

-o,--outdir

Path of the directory to place the program output.

-c, --config

Currently this program does NOT make use of a configuration file. This will be a fairly easy thing to add, and is on my TODO List.


OPTIONS

--genemark-dir

Directory that contains the GeneMark.hmm binaries. This can also be set with the environment variable GM_BIN_DIR.

--lib-dir

The full path to the directory that contains the model libraries for GeneMarkHMM. This can also be set with the environment varaible GM_LIB_DIR.

--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.

-q,--quiet

Run the program with minimal output.

--test

Run the program without doing the system commands.


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

Configuration File

The batch_genemark.pl program does not currently make use of a configuration file.

User Environment

This program makes use of the following variables defined in the user's environment.

GM_BIN_DIR

Directory that contains the GeneMark.hmm binaries.

GM_LIB_DIR

The full path to the directory that contains the model libraries for GeneMarkHMM.

The following example illustrates the ENV options set in the bash shell.

    export GM_BIN_DIR='$HOME/apps/GenMark/genemark_hmm_euk.linux/'
    export GM_LIB_DIR='$HOME/apps/GenMark/genemark_hmm_euk.linux/'


DEPENDENCIES

Required Software

Required Perl Modules


BUGS AND LIMITATIONS

Bugs

Limitations


SEE ALSO

The batch_genemark.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.


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: 11/09/2007

UPDATED: 03/24/2009

VERSION: $Rev: 555 $

 batch_genemark.pl