This directory contains applications that are built using software in CCTools.

The applications are grouped according to the software used in building and
running them:
1. Makeflow: makeflow_blast, makeflow_bwa
2. Parrot: parrot_atlas, parrot_cms
3. Work Queue: wq_maker, wq_replica_exchange, wq_sort


makeflow_blast
--------------------

The makeflow_blast program aligns a sequences of genomes listed in a fasta file
to the given database. The program uses the Makeflow framework for distributed
execution on available resources.

The README file in makeflow_blast/ contains instructions on how to run this
application.

makeflow_bwa
--------------------
The makeflow_bwa program aligns genome sequences listed in a fastq file to the
given a fasta reference. It uses the Burrows-Wheeler Aligner. The program uses
the Makeflow framework for distributed execution on available resources.

The README file in makeflow_bwa/ contains instructions on how to run this
application.

makeflow_gatk
--------------------
The makeflow_gatk program that uses walkers to traverse genome sequences in a
SAM/BAM file given a fasta reference performing variant calling. The program uses
the Makeflow framework for distributed execution on available resources.

The README file in makeflow_gatk/ contains instructions on how to run this
application.

parrot_atlas
--------------------
This program is an example of running a ATLAS simulation job using
the CVMFS filesystem accessed via Parrot.

The README file in parrot_atlas/ contains instructions on how to run this
application.

parrot_cms
--------------------
This program is an example of running a CMS simulation job using
the CVMFS filesystem accessed via Parrot.

The README file in parrot_cms/ contains instructions on how to run this
application.

wq_maker
--------------------

The wq_maker program annotates large sequences of genomes by harnessing
distributed compute resources. It uses the Work Queue framework for distributed
execution on available resources.

The README file in wq_maker/ contains instructions on how to run this
application.

wq_replica_exchange
--------------------
The wq_replica_exchange program runs the replica exchange molecular dynamics
simulations using the Work Queue framework.

The README file in wq_replica_exchange/ contains instructions on how to run this
application.

wq_sort
--------------------
The wq_sort program sorts a column of integers in a file by partitioning the
file into pieces and distributing them for individual sorting. The program uses
the Work Queue framework for distributed execution on available resources.

The README file in wq_sort/ contains instructions on how to run this
application.