[Bioperl-pipeline] new scripts

[Xiao Juguang]

Hi guys,

The 2 old scripts, PipelineManager.pl and Xml2DB.pl have been modulized and replaced with new names.

PipelineManager.pl is replaced with manager.pl, using the new module Bio::Pipeline::Manager. While Xml2DB.pl is replaced with importer.pl, using Bio::Pipeline::XMLImporter. The command-line argument forms remain unchanged, respectively.

The general principle of the modulization, same as the definition of the module's interface to script, is that script is just in charge of  fetching the default setting from Bio::Pipeline::PipeConf, parsing and checking the command-line arguments, and leaving the pipeline business logic work in the module under the package Bio::Pipeline. 

For scripts, they validate user's argument. If validation goes failed or user use -help, the scripts simple display the instructions and exits.

For modules, the constructor subs will take in the essential information that they need, mainly db login information. the sub 'run' is the main body to execute the task.

They are all tested and wait for your new pipeline. :)

Juguang.