Split libraries fastq

Adds the StudyPreprocesser class, which allows to preprocess the raw data of a study. Currently, it only supports Illumina data, but the code should be easy to expand to support other types.

I've also modified the `insert_filepaths` function, so it now supports to pass the filepath type either by id or by the string (name).

I've modified the initialize.sql file, to support the correct filetypes for the Illumina data and its preprocessed data. I had to modify multiple files due to this change.
But how will Travis handle it?

On Mon, Oct 13, 2014 at 8:33 AM, josenavas <notifications@github.com> wrote:

> In qiita_core/configuration_manager.py:
>
> > @@ -124,6 +126,11 @@ def _get_main(self, config):
> >              raise ValueError("The UPLOAD_DATA_DIR (%s) folder doesn't exist" %
> >                               self.upload_data_dir)
> >
> > +        self.working_dir = config.get('main', 'WORKING_DIR')
> > +        if not isdir(self.upload_data_dir):
> > +            raise ValueError("The WORKING_DIR (%s) folder doesn't exist" %
> > +                             self.upload_data_dir)
> > +
>
> I would suggest to have it always defined on the config file...
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/qiita/pull/353/files#r18776127>.
>