Create script to automate converting CORSIKA results to HDF5

Takes care of looking for already processed simulations,
simulations it already submitted to Stoomboot to be processed.
Submits jobs to Stoomboot to process events.
One job per simulation.
Fix bad syntax
Converted qsub store script to executable script

Add available slots in queue check
Add `source activate env` to ensure proper paths
Submit as many seeds as there are, or as many slots are available,
which ever is the lower number.
Also add script to setup.py
Add logging and progressbar to qsub store script
Improve qsub store data

Remove progress bar, improve logging, keep free slots in queue
Make progressbar optional for store_corsika_data
Store attributes on the file root instead of table

Storing attributes on the file root speeds up the read out.
Now you do not need to get the groundparticles node first.
Problem described in a comment in #18

Show no progressbar when there are only one or no particles.
Since progressbar does not like a maxval of 0.
Add cleanup to qsub_store_corsika_data

Remove script after submitting to Stoomboot.
Add flushing every Mrows

Additional flushing might prevent memory issues, though I believe
PyTables automatically flushes after many rows.
Remove an 'unused' flush.
Slightly more efficient if statement for progressbar updating.
Make CORSIKA reader more readable

Fixed all PEP8 issues in reader.py
Removed some duplicate code.
PEP8 fixes to whole of sapphire

Still some long lines left, but most offenders have been fixed
Shrink CORSIKA Stoomboot script

Remove some unnecessary echo statements and blank lines
Merge pull request #20 from HiSPARC/qsub_corsika_to_h5

Automate the conversion from DAT000000 to corsika.h5