Increasing the robustness of file parsing

I've been running into problems where the GFF information can't be formatted cleanly into HDF5 format, and so this release includes a lot of optimizations that I'm hoping will help for those failure cases which I'm having trouble pinpointing.

Add the bucket command wrapper

Add a small utility to make it easier to dispatch jobs from sciluigi

Add HDF5 output file

In addition to all of the other outputs, this release also includes an HDF5 output file for rapid querying of individual contigs or clusters.

Based on my experience with the previous release, I think that this is in good condition to use in a production setting.

Fix GFF parsing bug

Also added orientation information for cluster neighbors in JSON and SIF output files

Initial working version

Passes tests using small files in the tests/ folders. More testing is needed to see how it scales on large datasets.