Initial commit of the artifact project.
Fixed a bug with outputing the usage information.

Also project name is now called RAMPART (Robust and Automatic First Pass Assembly Tool)
Assembler script: Added command line argument to control memory and verbose output.  Also made better use of constants throughout.
Added the sequence info binary which I took from ~pachorip/clc/clc-ngs-cell-3.0.0beta2-linux_64/sequence_info.

Also modified the build.sh file which copies all resources necessary to make RAMPART run to the bin directory.
Added POD Usage to the perl script and reworked the way command line options are processed.

Also added a new parameter so that the script will run without submitting assembly jobs to the cluster.
Added scripts to gather and format statistics from a set of assemblies.
Added a collections of scripts to handle assembly analysis of a set of runs for both the raw and qt datasets.

Also renamed the R script that plots assembly statistics
Updated build.sh with additional assembly analysis scripts
Added basic functionality to R script, that merges the two tables (raw and quality trimmed) together
Added normalisation to assembly stats decider.
Finished the first cut of the assembly stats decider code.   Weightings are hardcoded for the time being.  It might make sense to add this as a user parameter later.
Removed Gap closing from the scaffolding script.

Added better cmd line option handling and usage info.

Started to work on script layout so it could accomodate other scaffolding tool.
Made some tweaks to scaffolder.

Added gap_closer, which is essentially a handy wrapper for any Gap Closing programs we may have. (Not tested yet!)
Fixed a bug with gap closer which prevented it from running correctly when the wait argument was empty.

Made stubs for additional scaffolding and gap closing tools.
Added additional cmd option to let user specify the job prefix for each assembly job
Stats gathered now uses strict grammar.
Renamed gap_closer to degap, and added stub for additional tool: GapFiller.
Start of a new script which should call other scripts to process raw and quality trimmed reads to produce a first pass assembly.
Added cmd line option to all scaffolder to run only after a job has completed.
Made assembler use strict grammar.