The wq_bowtie program aligns sequences of genomes listed in a fastq file using
Bowtie. It aligns by partitioning the file into pieces containing one or more
sequences and running Bowtie to align them individually. The program uses the
Work Queue framework for distributed execution.

To run:

1. Install CCTools.
2. Install Bowtie and all its required dependencies. Bowtie can be download from:
http://bowtie-bio.sourceforge.net/index.shtml
3. Run './wq_bowtie <REFERENCE_FILE> <FASTQ_FILE>' to align sequences in <FASTQ_FILE>.
4. 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_bowtie <REFERENCE_FILE> <FASTQ_FILE> -N WQBOWTIE
2. work_queue_worker -d all -N WQBOWTIE

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

When the alignment completes, you will find the output files in the
same directory from where wq_bowtie was run.
