Updating to Reggie 4.33

A. Before updating Reggie

1. New pipeline script

The readlength_averager.awk script is a new script that must be installed (see #1335). Install the script at a suitable location and make sure to update reggie-config.xml with the new path.

2. Create a new Tophat software alignment item

A new software item for the Tophat alignment is needed since the --mate-inner-dist parameter is calculated base on ReadLengthAvgR1 and ReadLengthAvgR2 annotations instead of ReadString. The new software items should be included as a project default and the old software item should be removed and SCAN-B access should be changed to Read-only (used to be Read-Use).