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.
Actually, it is defined in both files as empty string
<https://github.com/biocore/qiita/blob/master/qiita_core/support_files/config_test.txt#L25>,
which is then caught in the configuration manager and set
<https://github.com/biocore/qiita/blob/master/qiita_core/configuration_manager.py#L112-L116>
to the default directory.  The default directory for the working directory
should be

join(abspath(__file__), '..', 'qiita_db', 'support_files', 'work_data').

On Mon, Oct 13, 2014 at 9:35 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)
> > +
>
> We don't have a default config file for Qiita? i.e. how Travis is handling
> all the other directories? I just did the same that is done for all the
> other ones. on the config_test.txt and the config_demo.txt config files it
> is defined to /tmp/
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/qiita/pull/353/files#r18779576>.
>