Updating to Reggie 3.2

1. Picard and pipeline scripts should be updated

Ticket #742 (Detect tiles with empty barcode files) will not work without upgrading to Picard 1.128-4 on the Open grid cluster. See ​http://dev.thep.lu.se/basehacks/wiki/Picard for downloading and more information.

Note that this Picard version no longer ships each tool as a separate JAR file. All tools are packages together in picard.jar. Due to this change the command line to start Picard has changed (see ​http://dev.thep.lu.se/basehacks/wiki/Picard/notes3) and the pipeline scripts (​http://baseplugins.thep.lu.se/browser/other/pipeline/trunk) must also be updated (trunk revision 3099 or later). Note that the new pipeline scripts doesn't work with earlier version of Picard.

2. New role: PrepCurator

This role is needed to use the Flagged RNA wizard (#455). Assign users to this role as needed.