The makeflow_blast program aligns a sequences of genomes listed in a fasta file
to the given database. It aligns by partitioning the file into pieces containing
one or more sequences and distributing them for individual alignment. The
program uses the Makeflow framework for distributed execution on available
resources.

To build Makeflow:

1. Install BLAST and all its required dependencies. BLAST can be downloaded from:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
2. Install CCTools.
3. Copy makeflow_blast from cctools/apps to the location the makeflow will be executed.
4. Run './makeflow_blast -p blastx -d database_name -i input.fa -o output.txt --makeflow blast_makeflow'
This produces a file called blast_makeflow.

To run:

1. Run 'makeflow'
Note if the --makeflow option is specified with a MAKEFLOWFILE, run
makeflow blast_makeflow

This step runs the makeflow locally on the machine on which it is executed.

2. If you want to run with a distributed execution engine (Work Queue, Condor,
or SGE), specify the '-T' option. For example, to run with Work Queue,
makeflow blast_makeflow -T wq

3. Start Workers
work_queue_workers -d all <HOSTNAME> <PORT>
where <HOSTNAME> is the name of the host on which the master is running
	  <PORT> is the port number on which the master is listening.

Alternatively, you can also specify a project name for the master and use that
to start workers:
1. makeflow blast_makeflow -T wq -N BLAST
2. work_queue_worker -d all -N BLAST

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

When the alignment completes, you will find the whole output from the individual partitions
in the directory the makeflow was run in.
