The wq_maker program annotates sequences of genomes listed in a fasta file. It
annotates by partitioning the file into pieces containing one or more sequences
and distributing them for individual annotation. The program uses the Work Queue
framework for distributed execution on available resources.

The latest version of MAKER includes several updates and changes to the
implementation. The wq_maker.2_38 program runs with MAKER 2.38. Please note that
this program has been minimally tested and may contain bugs.

To run:

1. Install CCTools.
2. Instal MAKER and all its required dependencies. MAKER can be download from:
http://gmod.org/wiki/MAKER
3. Install wq_maker in the bin directory of the MAKER installation.
4. Run './wq_maker -g <FASTA_FILE' to annotate sequences in file <FASTA_FILE>.
5. Start workers:
work_queue_worker -d all <HOSTNAME> <PORT>
where <HOSTNAME> is the name of the host on which the manager is running
	  <PORT> is the port number on which the manager is listening.

Alternatively, you can also specify a project name for the manager and use that
to start workers:

1. ./wq_maker -g agambiae.fa -N WQMAKER
2. work_queue_worker -d all -N WQMAKER

For listing the command-line options, do:
./wq_maker -h

When the annotation completes, you will find the (.gff) output files in the
directory agambiae.maker.output which is created in the same directory as where
wq_maker was run.
