karinils/phylota — pull request #4 by rvosa (2012-05-28 11:39:29+00:00)
Title: New changes to merge with yours

I made some more changes, after you merge this pull request with your repository the following will have changed:

* I removed the old README.md (md=markdown) file. From now on we will only use the README.txt, which you will need to fill with the appropriate information: http://en.wikipedia.org/wiki/README

* I created placeholder data folders into which we will download GenBank flat files and taxonomy files

* I removed some silly old scripts

* IMPORTANTLY: I added POD documentation to DAO.pm. Have a look at lines 20-37 (starting with =head1, ending with =cut). These are written using Plain Old Documentation formatting (http://perldoc.perl.org/perlpod.html).

Your homework: read up on POD (http://perldoc.perl.org/perlpod.html) and on the sections I've added to DAO.pm (i.e. NAME and DESCRIPTION). Add similar sections to all the Domain and Service packages you have created. This means that you need think about what these packages are supposed to do, in general terms. You might be able to understand what to write by looking in the Functions google doc, otherwise ask Alex or me. Remember that the Domain packages are going to represent the data, and the Service packages are going to represent operations that can be performed on the data.

More homework: start filling the README.txt with a general description of the project, how the steps in the pipeline are supposed to fit together, and what the goals (end results) of the project are.